Starting phenix.real_space_refine on Sat Mar 23 06:04:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6htq_0270/03_2024/6htq_0270.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6htq_0270/03_2024/6htq_0270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6htq_0270/03_2024/6htq_0270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6htq_0270/03_2024/6htq_0270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6htq_0270/03_2024/6htq_0270.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6htq_0270/03_2024/6htq_0270.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4766 5.49 5 S 140 5.16 5 C 73413 2.51 5 N 27229 2.21 5 O 41132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 108": "NH1" <-> "NH2" Residue "O ARG 97": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "P ARG 14": "NH1" <-> "NH2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 39": "NH1" <-> "NH2" Residue "P ARG 93": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ARG 75": "NH1" <-> "NH2" Residue "R ARG 89": "NH1" <-> "NH2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "V ARG 28": "NH1" <-> "NH2" Residue "V TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "Z PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 22": "NH1" <-> "NH2" Residue "b ARG 29": "NH1" <-> "NH2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ARG 143": "NH1" <-> "NH2" Residue "b ARG 167": "NH1" <-> "NH2" Residue "b ARG 170": "NH1" <-> "NH2" Residue "b ARG 177": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "d TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "d ARG 146": "NH1" <-> "NH2" Residue "e ARG 20": "NH1" <-> "NH2" Residue "e ARG 32": "NH1" <-> "NH2" Residue "e ARG 112": "NH1" <-> "NH2" Residue "f ARG 11": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f ARG 77": "NH1" <-> "NH2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g ARG 79": "NH1" <-> "NH2" Residue "g ARG 92": "NH1" <-> "NH2" Residue "g ARG 111": "NH1" <-> "NH2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "h ARG 61": "NH1" <-> "NH2" Residue "h ARG 96": "NH1" <-> "NH2" Residue "h ARG 119": "NH1" <-> "NH2" Residue "i ARG 12": "NH1" <-> "NH2" Residue "i ARG 20": "NH1" <-> "NH2" Residue "i TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i ARG 109": "NH1" <-> "NH2" Residue "i ARG 113": "NH1" <-> "NH2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 9": "NH1" <-> "NH2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "k ARG 26": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 63": "NH1" <-> "NH2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l ARG 123": "NH1" <-> "NH2" Residue "m ARG 3": "NH1" <-> "NH2" Residue "m ARG 11": "NH1" <-> "NH2" Residue "m ARG 27": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 79": "NH1" <-> "NH2" Residue "m ARG 93": "NH1" <-> "NH2" Residue "m ARG 107": "NH1" <-> "NH2" Residue "m ARG 109": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 19": "NH1" <-> "NH2" Residue "p ARG 29": "NH1" <-> "NH2" Residue "p ARG 32": "NH1" <-> "NH2" Residue "p ARG 71": "NH1" <-> "NH2" Residue "q ARG 39": "NH1" <-> "NH2" Residue "q ARG 67": "NH1" <-> "NH2" Residue "r ARG 48": "NH1" <-> "NH2" Residue "t ARG 18": "NH1" <-> "NH2" Residue "t ARG 78": "NH1" <-> "NH2" Residue "x ARG 418": "NH1" <-> "NH2" Residue "x ARG 444": "NH1" <-> "NH2" Residue "x ARG 478": "NH1" <-> "NH2" Residue "x ARG 485": "NH1" <-> "NH2" Residue "x ARG 486": "NH1" <-> "NH2" Residue "x ARG 494": "NH1" <-> "NH2" Residue "x ARG 549": "NH1" <-> "NH2" Residue "x ARG 555": "NH1" <-> "NH2" Residue "x ARG 558": "NH1" <-> "NH2" Residue "x ARG 581": "NH1" <-> "NH2" Residue "x ARG 583": "NH1" <-> "NH2" Residue "x ARG 588": "NH1" <-> "NH2" Residue "x ARG 598": "NH1" <-> "NH2" Residue "x ARG 639": "NH1" <-> "NH2" Residue "x ARG 654": "NH1" <-> "NH2" Residue "x ARG 668": "NH1" <-> "NH2" Residue "x ARG 669": "NH1" <-> "NH2" Residue "x ARG 695": "NH1" <-> "NH2" Residue "x ARG 719": "NH1" <-> "NH2" Residue "x ARG 731": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 146680 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 61997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2887, 61997 Inner-chain residues flagged as termini: ['pdbres=" G A 328 "', 'pdbres=" G A1220 "'] Classifications: {'RNA': 2887} Modifications used: {'5*END': 3, 'rna2p_pur': 296, 'rna2p_pyr': 161, 'rna3p_pur': 1381, 'rna3p_pyr': 1048} Link IDs: {'rna2p': 457, 'rna3p': 2429} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 97} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "E" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "F" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "G" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1081 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "M" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "O" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "P" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 944 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "U" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "V" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "W" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "X" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "Y" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "1" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "2" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "3" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "4" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "5" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "Z" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 499 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "a" Number of atoms: 32891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32891 Classifications: {'RNA': 1533} Modifications used: {'rna2p_pur': 116, 'rna2p_pyr': 86, 'rna3p_pur': 754, 'rna3p_pyr': 577} Link IDs: {'rna2p': 201, 'rna3p': 1331} Chain: "b" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1757 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 3, 'TRANS': 202} Chain: "d" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1568 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "e" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1218 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "f" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 755 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1181 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "h" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1036 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "i" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "j" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 761 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "k" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 838 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "l" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1052 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "m" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 868 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "n" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 497 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "p" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "q" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 691 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "r" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "s" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 637 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "v" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1861 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 40, 'rna3p_pyr': 36} Link IDs: {'rna2p': 10, 'rna3p': 76} Chain: "x" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2752 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 327} Chain: "u" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'rna2p': 16, 'rna3p': 59} Chain: "w" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1599 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 11, 'rna3p': 63} Time building chain proxies: 57.70, per 1000 atoms: 0.39 Number of scatterers: 146680 At special positions: 0 Unit cell: (269.916, 275.336, 223.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 4766 15.00 O 41132 8.00 N 27229 7.00 C 73413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 1 30 " - pdb=" SG CYS 1 43 " distance=2.05 Simple disulfide: pdb=" SG CYS 1 33 " - pdb=" SG CYS 1 46 " distance=2.02 Simple disulfide: pdb=" SG CYS n 27 " - pdb=" SG CYS n 43 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 68.15 Conformation dependent library (CDL) restraints added in 7.1 seconds 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10338 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 77 sheets defined 33.1% alpha, 15.5% beta 1051 base pairs and 2347 stacking pairs defined. Time for finding SS restraints: 48.42 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.557A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.662A pdb=" N VAL D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.597A pdb=" N ALA D 90 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 removed outlier: 4.207A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 29 through 41 removed outlier: 3.548A pdb=" N VAL E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 38 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 45 Processing helix chain 'E' and resid 102 through 121 removed outlier: 3.758A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 removed outlier: 3.558A pdb=" N MET E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.658A pdb=" N VAL E 187 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 removed outlier: 3.694A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 21 removed outlier: 3.581A pdb=" N THR F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 4.562A pdb=" N ALA F 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 52 removed outlier: 3.936A pdb=" N ASP F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 52' Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 93 through 106 removed outlier: 4.043A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.589A pdb=" N THR F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.698A pdb=" N ALA G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG G 70 " --> pdb=" O HIS G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 removed outlier: 4.511A pdb=" N ALA G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 39 removed outlier: 4.379A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA J 35 " --> pdb=" O SER J 31 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 63 Processing helix chain 'J' and resid 68 through 73 removed outlier: 3.763A pdb=" N LYS J 73 " --> pdb=" O LYS J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 103 through 108 removed outlier: 4.043A pdb=" N GLY J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.838A pdb=" N ARG J 117 " --> pdb=" O GLY J 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 107 removed outlier: 3.611A pdb=" N LEU K 106 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG K 107 " --> pdb=" O ARG K 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 103 through 107' Processing helix chain 'K' and resid 111 through 117 Processing helix chain 'L' and resid 2 through 6 removed outlier: 4.247A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.518A pdb=" N ARG L 41 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 85 Processing helix chain 'L' and resid 92 through 99 removed outlier: 3.507A pdb=" N LEU L 97 " --> pdb=" O PRO L 93 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 139 removed outlier: 3.551A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU L 137 " --> pdb=" O LYS L 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 59 removed outlier: 4.019A pdb=" N ALA M 50 " --> pdb=" O GLN M 46 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET M 58 " --> pdb=" O MET M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 118 removed outlier: 3.773A pdb=" N GLU M 116 " --> pdb=" O GLU M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 123 removed outlier: 3.844A pdb=" N HIS M 123 " --> pdb=" O ARG M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 18 removed outlier: 3.664A pdb=" N ARG N 13 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS N 14 " --> pdb=" O SER N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 27 removed outlier: 4.026A pdb=" N THR N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU N 24 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 43 through 54 removed outlier: 4.052A pdb=" N THR N 49 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY N 51 " --> pdb=" O MET N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 66 removed outlier: 3.758A pdb=" N GLN N 61 " --> pdb=" O HIS N 57 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA N 64 " --> pdb=" O ARG N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 86 removed outlier: 3.635A pdb=" N LEU N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP N 86 " --> pdb=" O LYS N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 91 Processing helix chain 'O' and resid 6 through 20 removed outlier: 3.695A pdb=" N ARG O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG O 17 " --> pdb=" O LYS O 13 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 88 removed outlier: 3.749A pdb=" N GLU O 79 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA O 82 " --> pdb=" O GLY O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 117 Processing helix chain 'P' and resid 2 through 7 Processing helix chain 'P' and resid 8 through 13 removed outlier: 3.920A pdb=" N GLU P 11 " --> pdb=" O ILE P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 56 Processing helix chain 'P' and resid 97 through 102 Processing helix chain 'Q' and resid 14 through 19 Processing helix chain 'Q' and resid 25 through 29 removed outlier: 3.563A pdb=" N LYS Q 28 " --> pdb=" O PHE Q 25 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 25 through 29' Processing helix chain 'Q' and resid 31 through 49 removed outlier: 4.117A pdb=" N GLN Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET Q 40 " --> pdb=" O ASN Q 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS Q 41 " --> pdb=" O GLN Q 37 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN Q 44 " --> pdb=" O MET Q 40 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR Q 45 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 55 Processing helix chain 'Q' and resid 57 through 71 removed outlier: 4.356A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG Q 64 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.543A pdb=" N LEU Q 79 " --> pdb=" O SER Q 75 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU Q 85 " --> pdb=" O HIS Q 81 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 101 removed outlier: 3.612A pdb=" N ASP Q 97 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU Q 98 " --> pdb=" O MET Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 118 removed outlier: 3.505A pdb=" N ASN Q 107 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN Q 108 " --> pdb=" O THR Q 104 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA Q 112 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA Q 113 " --> pdb=" O LEU Q 109 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 17 Processing helix chain 'S' and resid 19 through 23 Processing helix chain 'S' and resid 28 through 36 removed outlier: 4.436A pdb=" N SER S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 61 removed outlier: 3.845A pdb=" N ILE S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS S 49 " --> pdb=" O PRO S 45 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA S 56 " --> pdb=" O LYS S 52 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'T' and resid 3 through 6 Processing helix chain 'T' and resid 14 through 21 Processing helix chain 'T' and resid 35 through 47 removed outlier: 3.710A pdb=" N GLU T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 7 removed outlier: 3.536A pdb=" N ARG X 7 " --> pdb=" O ALA X 3 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 35 removed outlier: 3.950A pdb=" N ARG X 29 " --> pdb=" O LEU X 25 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE X 30 " --> pdb=" O PHE X 26 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN X 31 " --> pdb=" O ASN X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 39 through 65 removed outlier: 4.140A pdb=" N ILE X 43 " --> pdb=" O ASN X 39 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG X 44 " --> pdb=" O THR X 40 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG X 52 " --> pdb=" O LYS X 48 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET X 53 " --> pdb=" O ALA X 49 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL X 56 " --> pdb=" O ARG X 52 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE X 57 " --> pdb=" O MET X 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 26 removed outlier: 3.543A pdb=" N VAL Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR Y 22 " --> pdb=" O ASP Y 18 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL Y 23 " --> pdb=" O GLN Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.530A pdb=" N MET Y 46 " --> pdb=" O ALA Y 42 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 14 Processing helix chain '3' and resid 25 through 38 removed outlier: 3.715A pdb=" N LEU 3 29 " --> pdb=" O LYS 3 25 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL 3 30 " --> pdb=" O ASN 3 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU 3 31 " --> pdb=" O GLY 3 27 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY 3 38 " --> pdb=" O ARG 3 34 " (cutoff:3.500A) Processing helix chain '4' and resid 7 through 11 Processing helix chain '4' and resid 37 through 44 removed outlier: 3.755A pdb=" N LYS 4 41 " --> pdb=" O SER 4 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS 4 43 " --> pdb=" O LYS 4 39 " (cutoff:3.500A) Processing helix chain '4' and resid 51 through 59 removed outlier: 3.978A pdb=" N LYS 4 56 " --> pdb=" O ALA 4 52 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG 4 57 " --> pdb=" O GLY 4 53 " (cutoff:3.500A) Processing helix chain '5' and resid 29 through 32 Processing helix chain 'Z' and resid 47 through 54 removed outlier: 3.733A pdb=" N SER Z 51 " --> pdb=" O GLN Z 47 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA Z 52 " --> pdb=" O LYS Z 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 removed outlier: 3.514A pdb=" N LYS b 28 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG b 29 " --> pdb=" O LYS b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 62 removed outlier: 3.612A pdb=" N GLU b 52 " --> pdb=" O LYS b 48 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS b 58 " --> pdb=" O TYR b 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN b 59 " --> pdb=" O ASN b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 88 removed outlier: 4.216A pdb=" N SER b 79 " --> pdb=" O GLN b 75 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS b 81 " --> pdb=" O GLN b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 123 removed outlier: 3.761A pdb=" N GLU b 118 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS b 119 " --> pdb=" O LYS b 115 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET b 120 " --> pdb=" O ASP b 116 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU b 122 " --> pdb=" O GLU b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 136 Processing helix chain 'b' and resid 136 through 148 removed outlier: 3.650A pdb=" N LYS b 146 " --> pdb=" O GLU b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 149 through 152 removed outlier: 3.630A pdb=" N LYS b 152 " --> pdb=" O GLY b 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 149 through 152' Processing helix chain 'b' and resid 169 through 179 removed outlier: 4.067A pdb=" N VAL b 173 " --> pdb=" O GLU b 169 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU b 175 " --> pdb=" O ILE b 171 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA b 176 " --> pdb=" O ALA b 172 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 224 removed outlier: 3.576A pdb=" N THR b 214 " --> pdb=" O VAL b 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 3.828A pdb=" N LEU c 32 " --> pdb=" O TYR c 28 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU c 34 " --> pdb=" O ASP c 30 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE c 38 " --> pdb=" O GLU c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.836A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA c 85 " --> pdb=" O SER c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 Processing helix chain 'c' and resid 111 through 125 removed outlier: 3.542A pdb=" N ASP c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE c 119 " --> pdb=" O VAL c 115 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 4.086A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 16 removed outlier: 3.773A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 3.521A pdb=" N LEU d 51 " --> pdb=" O TYR d 47 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN d 52 " --> pdb=" O GLY d 48 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU d 57 " --> pdb=" O GLU d 53 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N MET d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 75 removed outlier: 4.055A pdb=" N THR d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU d 71 " --> pdb=" O GLN d 67 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE d 72 " --> pdb=" O PHE d 68 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 90 removed outlier: 3.607A pdb=" N LEU d 90 " --> pdb=" O PHE d 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 108 through 116 removed outlier: 3.967A pdb=" N GLN d 112 " --> pdb=" O ARG d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 142 through 146 Processing helix chain 'd' and resid 148 through 157 Processing helix chain 'd' and resid 181 through 186 Processing helix chain 'd' and resid 193 through 198 Processing helix chain 'e' and resid 56 through 70 removed outlier: 3.666A pdb=" N ILE e 60 " --> pdb=" O VAL e 56 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL e 64 " --> pdb=" O ILE e 60 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU e 65 " --> pdb=" O ARG e 61 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP e 66 " --> pdb=" O LYS e 62 " (cutoff:3.500A) Processing helix chain 'e' and resid 76 through 80 Processing helix chain 'e' and resid 108 through 116 removed outlier: 3.811A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU e 116 " --> pdb=" O ARG e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 146 removed outlier: 3.638A pdb=" N GLN e 142 " --> pdb=" O ARG e 138 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY e 143 " --> pdb=" O ALA e 139 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 removed outlier: 3.639A pdb=" N ALA e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 166 removed outlier: 3.541A pdb=" N LEU e 164 " --> pdb=" O SER e 160 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU e 165 " --> pdb=" O VAL e 161 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 34 removed outlier: 3.528A pdb=" N ALA f 21 " --> pdb=" O GLU f 17 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN f 33 " --> pdb=" O VAL f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 80 removed outlier: 3.659A pdb=" N ASP f 76 " --> pdb=" O VAL f 72 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG f 77 " --> pdb=" O GLN f 73 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU f 78 " --> pdb=" O GLU f 74 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA f 79 " --> pdb=" O PHE f 75 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS f 80 " --> pdb=" O ASP f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 29 removed outlier: 3.605A pdb=" N ARG g 25 " --> pdb=" O LYS g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 36 through 54 removed outlier: 3.573A pdb=" N ILE g 42 " --> pdb=" O LYS g 38 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS g 45 " --> pdb=" O THR g 41 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE g 49 " --> pdb=" O LYS g 45 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR g 54 " --> pdb=" O ILE g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 68 removed outlier: 3.804A pdb=" N GLN g 64 " --> pdb=" O GLU g 60 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN g 68 " --> pdb=" O GLN g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 4.027A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY g 100 " --> pdb=" O ARG g 96 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU g 101 " --> pdb=" O THR g 97 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR g 107 " --> pdb=" O TRP g 103 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 129 removed outlier: 3.780A pdb=" N ALA g 121 " --> pdb=" O GLU g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 removed outlier: 3.689A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS g 137 " --> pdb=" O ALA g 133 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG g 138 " --> pdb=" O ALA g 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR g 141 " --> pdb=" O LYS g 137 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 151 No H-bonds generated for 'chain 'g' and resid 149 through 151' Processing helix chain 'h' and resid 7 through 19 removed outlier: 3.892A pdb=" N ARG h 13 " --> pdb=" O ASP h 9 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET h 19 " --> pdb=" O ARG h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 43 removed outlier: 3.603A pdb=" N GLU h 38 " --> pdb=" O ARG h 34 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.571A pdb=" N ALA h 118 " --> pdb=" O THR h 114 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS h 121 " --> pdb=" O GLU h 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 41 through 49 removed outlier: 3.843A pdb=" N ILE i 45 " --> pdb=" O SER i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 55 removed outlier: 3.764A pdb=" N LEU i 54 " --> pdb=" O GLN i 50 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 89 removed outlier: 3.810A pdb=" N HIS i 81 " --> pdb=" O GLY i 77 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA i 84 " --> pdb=" O ARG i 80 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 101 removed outlier: 3.504A pdb=" N ALA i 101 " --> pdb=" O THR i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 21 Processing helix chain 'j' and resid 21 through 32 removed outlier: 4.022A pdb=" N ILE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR j 28 " --> pdb=" O LYS j 24 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 89 removed outlier: 3.636A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 53 Processing helix chain 'k' and resid 56 through 60 removed outlier: 3.931A pdb=" N LYS k 59 " --> pdb=" O GLY k 56 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER k 60 " --> pdb=" O SER k 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 56 through 60' Processing helix chain 'k' and resid 61 through 80 removed outlier: 3.815A pdb=" N GLU k 70 " --> pdb=" O GLN k 66 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY k 75 " --> pdb=" O THR k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 105 removed outlier: 3.616A pdb=" N GLN k 103 " --> pdb=" O ILE k 99 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA k 104 " --> pdb=" O ARG k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 9 removed outlier: 3.933A pdb=" N ARG l 9 " --> pdb=" O ASN l 5 " (cutoff:3.500A) Processing helix chain 'l' and resid 21 through 25 removed outlier: 3.944A pdb=" N LEU l 24 " --> pdb=" O SER l 21 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 132 removed outlier: 3.937A pdb=" N GLY l 131 " --> pdb=" O SER l 128 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR l 132 " --> pdb=" O LYS l 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 128 through 132' Processing helix chain 'm' and resid 14 through 20 removed outlier: 3.817A pdb=" N LEU m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 49 through 63 removed outlier: 3.648A pdb=" N LYS m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE m 56 " --> pdb=" O GLU m 52 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE m 59 " --> pdb=" O LYS m 55 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE m 60 " --> pdb=" O ILE m 56 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU m 63 " --> pdb=" O ILE m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 82 removed outlier: 3.904A pdb=" N VAL m 73 " --> pdb=" O LEU m 69 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER m 74 " --> pdb=" O ARG m 70 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU m 82 " --> pdb=" O LYS m 78 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 94 removed outlier: 4.152A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 110 removed outlier: 4.067A pdb=" N LYS m 110 " --> pdb=" O ARG m 107 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 11 removed outlier: 3.837A pdb=" N GLN n 10 " --> pdb=" O MET n 6 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 20 removed outlier: 3.545A pdb=" N GLU n 20 " --> pdb=" O LYS n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 49 removed outlier: 3.997A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU n 47 " --> pdb=" O CYS n 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 6 through 15 removed outlier: 3.989A pdb=" N ASN o 13 " --> pdb=" O ASN o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 25 through 46 removed outlier: 3.695A pdb=" N ALA o 30 " --> pdb=" O GLU o 26 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP o 34 " --> pdb=" O ALA o 30 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS o 42 " --> pdb=" O ASN o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 72 removed outlier: 4.147A pdb=" N ASN o 72 " --> pdb=" O THR o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 84 Processing helix chain 'p' and resid 54 through 63 removed outlier: 3.981A pdb=" N LYS p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP p 59 " --> pdb=" O LEU p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 removed outlier: 4.669A pdb=" N LEU p 73 " --> pdb=" O THR p 69 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE p 74 " --> pdb=" O VAL p 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 78 through 88 Processing helix chain 'r' and resid 16 through 22 removed outlier: 3.640A pdb=" N ASN r 21 " --> pdb=" O TYR r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 36 removed outlier: 3.808A pdb=" N LYS r 36 " --> pdb=" O ASP r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 69 removed outlier: 3.560A pdb=" N THR r 61 " --> pdb=" O GLN r 57 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS r 65 " --> pdb=" O THR r 61 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG r 66 " --> pdb=" O ALA r 62 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 4.243A pdb=" N THR s 25 " --> pdb=" O LYS s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 removed outlier: 3.864A pdb=" N ILE s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 75 removed outlier: 3.658A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA s 75 " --> pdb=" O GLY s 72 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 41 removed outlier: 4.022A pdb=" N THR t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU t 16 " --> pdb=" O LYS t 12 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS t 20 " --> pdb=" O GLU t 16 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 3.673A pdb=" N ARG t 57 " --> pdb=" O GLU t 53 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS t 60 " --> pdb=" O LYS t 56 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL t 62 " --> pdb=" O ILE t 58 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS t 63 " --> pdb=" O ASP t 59 " (cutoff:3.500A) Processing helix chain 't' and resid 69 through 86 removed outlier: 3.982A pdb=" N ARG t 74 " --> pdb=" O ASN t 70 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU t 79 " --> pdb=" O TYR t 75 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS t 82 " --> pdb=" O ARG t 78 " (cutoff:3.500A) Processing helix chain 'x' and resid 413 through 420 removed outlier: 4.113A pdb=" N TYR x 417 " --> pdb=" O ILE x 413 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG x 418 " --> pdb=" O ASP x 414 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE x 419 " --> pdb=" O PHE x 415 " (cutoff:3.500A) Processing helix chain 'x' and resid 420 through 426 removed outlier: 3.897A pdb=" N GLY x 424 " --> pdb=" O HIS x 420 " (cutoff:3.500A) Processing helix chain 'x' and resid 462 through 467 removed outlier: 3.540A pdb=" N VAL x 465 " --> pdb=" O GLN x 462 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS x 466 " --> pdb=" O ASP x 463 " (cutoff:3.500A) Processing helix chain 'x' and resid 470 through 481 Processing helix chain 'x' and resid 481 through 503 removed outlier: 4.183A pdb=" N GLU x 487 " --> pdb=" O LYS x 483 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU x 488 " --> pdb=" O GLN x 484 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU x 491 " --> pdb=" O GLU x 487 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS x 492 " --> pdb=" O GLU x 488 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE x 501 " --> pdb=" O VAL x 497 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS x 502 " --> pdb=" O GLU x 498 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN x 503 " --> pdb=" O LYS x 499 " (cutoff:3.500A) Processing helix chain 'x' and resid 516 through 521 removed outlier: 3.885A pdb=" N VAL x 520 " --> pdb=" O ILE x 517 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA x 521 " --> pdb=" O GLN x 518 " (cutoff:3.500A) Processing helix chain 'x' and resid 529 through 534 removed outlier: 3.526A pdb=" N TYR x 533 " --> pdb=" O GLU x 529 " (cutoff:3.500A) Processing helix chain 'x' and resid 534 through 539 removed outlier: 4.112A pdb=" N TYR x 538 " --> pdb=" O ALA x 534 " (cutoff:3.500A) Processing helix chain 'x' and resid 545 through 551 Processing helix chain 'x' and resid 557 through 570 Processing helix chain 'x' and resid 628 through 633 removed outlier: 3.660A pdb=" N THR x 633 " --> pdb=" O PRO x 629 " (cutoff:3.500A) Processing helix chain 'x' and resid 636 through 638 No H-bonds generated for 'chain 'x' and resid 636 through 638' Processing helix chain 'x' and resid 671 through 680 removed outlier: 3.658A pdb=" N VAL x 679 " --> pdb=" O VAL x 675 " (cutoff:3.500A) Processing helix chain 'x' and resid 709 through 718 removed outlier: 3.613A pdb=" N LYS x 715 " --> pdb=" O ASN x 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 82 removed outlier: 3.526A pdb=" N ILE C 94 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG C 102 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.626A pdb=" N LEU C 130 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LYS C 167 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 9 removed outlier: 7.136A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU D 175 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN D 173 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 13 through 16 removed outlier: 3.724A pdb=" N VAL D 25 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 15 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 50 Processing sheet with id=AA9, first strand: chain 'D' and resid 116 through 119 removed outlier: 5.742A pdb=" N MET D 164 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 6 through 7 removed outlier: 4.700A pdb=" N LEU E 6 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 123 through 125 removed outlier: 3.784A pdb=" N THR E 174 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 154 " --> pdb=" O THR E 174 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 66 through 70 removed outlier: 5.947A pdb=" N VAL F 66 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA F 87 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA F 70 " --> pdb=" O MET F 83 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N MET F 83 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 35 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET F 152 " --> pdb=" O ILE F 132 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE F 132 " --> pdb=" O MET F 152 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE F 154 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 9 through 10 Processing sheet with id=AB5, first strand: chain 'G' and resid 16 through 19 Processing sheet with id=AB6, first strand: chain 'G' and resid 123 through 125 Processing sheet with id=AB7, first strand: chain 'G' and resid 96 through 100 Processing sheet with id=AB8, first strand: chain 'J' and resid 123 through 126 removed outlier: 6.456A pdb=" N VAL J 55 " --> pdb=" O ASN J 124 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N TYR J 126 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE J 57 " --> pdb=" O TYR J 126 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE J 58 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP J 16 " --> pdb=" O GLU J 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 75 through 78 removed outlier: 3.637A pdb=" N ARG J 77 " --> pdb=" O LYS J 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.019A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N CYS K 84 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ILE K 86 " --> pdb=" O LYS K 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 77 through 78 removed outlier: 3.763A pdb=" N SER P 65 " --> pdb=" O VAL P 68 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 75 through 77 removed outlier: 5.382A pdb=" N ALA L 75 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL L 109 " --> pdb=" O LYS L 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'L' and resid 90 through 91 removed outlier: 6.004A pdb=" N VAL L 91 " --> pdb=" O LYS L 124 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA L 125 " --> pdb=" O GLU L 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 102 through 106 removed outlier: 6.759A pdb=" N ILE M 34 " --> pdb=" O LEU M 103 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU M 105 " --> pdb=" O PHE M 32 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE M 32 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN M 35 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 40 through 42 removed outlier: 3.896A pdb=" N SER M 40 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL M 97 " --> pdb=" O SER M 40 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA M 89 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA M 76 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP M 93 " --> pdb=" O LYS M 72 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LYS M 72 " --> pdb=" O TRP M 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 70 through 72 removed outlier: 6.677A pdb=" N GLN N 77 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 30 through 34 removed outlier: 7.157A pdb=" N ALA O 42 " --> pdb=" O SER O 55 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER O 55 " --> pdb=" O ALA O 42 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE O 44 " --> pdb=" O LEU O 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 38 through 46 removed outlier: 3.564A pdb=" N ARG P 39 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR P 25 " --> pdb=" O VAL P 87 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL P 87 " --> pdb=" O THR P 25 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 3 through 6 removed outlier: 3.656A pdb=" N ILE R 5 " --> pdb=" O ILE R 12 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE R 12 " --> pdb=" O ILE R 5 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.191A pdb=" N THR R 96 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL R 62 " --> pdb=" O THR R 96 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 71 through 74 removed outlier: 3.662A pdb=" N ILE R 71 " --> pdb=" O HIS R 88 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 5 through 6 removed outlier: 3.609A pdb=" N GLN S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER S 108 " --> pdb=" O ILE S 71 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AD6, first strand: chain 'S' and resid 82 through 86 Processing sheet with id=AD7, first strand: chain 'T' and resid 8 through 11 removed outlier: 3.963A pdb=" N ARG T 77 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 9 through 11 Processing sheet with id=AD9, first strand: chain 'U' and resid 23 through 27 Processing sheet with id=AE1, first strand: chain 'U' and resid 40 through 44 removed outlier: 3.534A pdb=" N GLN U 59 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 81 through 85 Processing sheet with id=AE3, first strand: chain 'V' and resid 30 through 31 removed outlier: 3.552A pdb=" N GLY V 30 " --> pdb=" O ARG V 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG V 47 " --> pdb=" O GLY V 30 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU V 67 " --> pdb=" O LEU V 45 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE V 68 " --> pdb=" O GLY V 60 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 53 through 57 removed outlier: 7.453A pdb=" N TYR V 54 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N VAL V 89 " --> pdb=" O TYR V 54 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLY V 56 " --> pdb=" O VAL V 89 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Y' and resid 35 through 38 Processing sheet with id=AE6, first strand: chain '1' and resid 27 through 29 Processing sheet with id=AE7, first strand: chain '1' and resid 48 through 49 removed outlier: 3.594A pdb=" N LYS 1 52 " --> pdb=" O TYR 1 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '2' and resid 18 through 21 removed outlier: 3.578A pdb=" N LYS 2 21 " --> pdb=" O VAL 2 3 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL 2 3 " --> pdb=" O LYS 2 21 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS 2 41 " --> pdb=" O CYS 2 36 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS 2 36 " --> pdb=" O LYS 2 41 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '4' and resid 23 through 25 Processing sheet with id=AF1, first strand: chain '5' and resid 2 through 3 removed outlier: 6.753A pdb=" N LYS 5 2 " --> pdb=" O LYS 5 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain '5' and resid 15 through 19 Processing sheet with id=AF3, first strand: chain 'Z' and resid 21 through 26 removed outlier: 3.715A pdb=" N VAL Z 31 " --> pdb=" O THR Z 13 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'b' and resid 31 through 33 Processing sheet with id=AF5, first strand: chain 'b' and resid 68 through 70 Processing sheet with id=AF6, first strand: chain 'b' and resid 162 through 163 removed outlier: 6.025A pdb=" N ILE b 163 " --> pdb=" O ILE b 186 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 20 through 21 removed outlier: 3.994A pdb=" N ARG c 58 " --> pdb=" O LYS c 21 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL c 63 " --> pdb=" O HIS c 99 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASN c 101 " --> pdb=" O VAL c 63 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE c 65 " --> pdb=" O ASN c 101 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE c 67 " --> pdb=" O LEU c 103 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 166 through 170 removed outlier: 3.541A pdb=" N THR c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL c 199 " --> pdb=" O ALA c 184 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'd' and resid 120 through 121 Processing sheet with id=AG1, first strand: chain 'd' and resid 165 through 167 removed outlier: 3.532A pdb=" N THR d 166 " --> pdb=" O THR d 175 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR d 175 " --> pdb=" O THR d 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'e' and resid 14 through 21 removed outlier: 5.276A pdb=" N LEU e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL e 38 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU e 36 " --> pdb=" O THR e 17 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE e 33 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA e 53 " --> pdb=" O PHE e 33 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL e 37 " --> pdb=" O GLY e 49 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY e 49 " --> pdb=" O VAL e 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'e' and resid 85 through 87 removed outlier: 3.944A pdb=" N LEU e 95 " --> pdb=" O LYS e 126 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS e 126 " --> pdb=" O LEU e 95 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'f' and resid 37 through 42 removed outlier: 3.640A pdb=" N GLY f 58 " --> pdb=" O ARG f 46 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'f' and resid 37 through 42 removed outlier: 3.568A pdb=" N GLN f 61 " --> pdb=" O TYR f 8 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG f 87 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'g' and resid 73 through 78 Processing sheet with id=AG7, first strand: chain 'h' and resid 46 through 52 removed outlier: 6.903A pdb=" N PHE h 63 " --> pdb=" O ARG h 47 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL h 49 " --> pdb=" O ARG h 61 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG h 61 " --> pdb=" O VAL h 49 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N PHE h 51 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE h 59 " --> pdb=" O PHE h 51 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'h' and resid 77 through 78 Processing sheet with id=AG9, first strand: chain 'h' and resid 88 through 89 removed outlier: 3.587A pdb=" N GLU h 126 " --> pdb=" O SER h 107 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'i' and resid 6 through 11 Processing sheet with id=AH2, first strand: chain 'j' and resid 7 through 12 removed outlier: 6.659A pdb=" N GLU j 63 " --> pdb=" O THR j 50 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N THR j 50 " --> pdb=" O GLU j 63 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE j 65 " --> pdb=" O VAL j 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL j 48 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET j 67 " --> pdb=" O LYS j 46 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS j 46 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR j 69 " --> pdb=" O THR j 44 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N THR j 44 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'j' and resid 7 through 12 Processing sheet with id=AH4, first strand: chain 'k' and resid 43 through 47 removed outlier: 6.552A pdb=" N LEU k 84 " --> pdb=" O VAL k 109 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA k 111 " --> pdb=" O LEU k 84 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'l' and resid 75 through 76 removed outlier: 3.860A pdb=" N LYS l 43 " --> pdb=" O ILE l 95 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG l 96 " --> pdb=" O HIS l 109 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS l 109 " --> pdb=" O ARG l 96 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'p' and resid 3 through 6 removed outlier: 3.551A pdb=" N LYS p 4 " --> pdb=" O ALA p 23 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA p 23 " --> pdb=" O LYS p 4 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'p' and resid 9 through 11 Processing sheet with id=AH8, first strand: chain 'q' and resid 9 through 14 removed outlier: 3.723A pdb=" N VAL q 25 " --> pdb=" O PHE q 46 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N LYS q 73 " --> pdb=" O LYS q 45 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS q 47 " --> pdb=" O LYS q 73 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG q 74 " --> pdb=" O THR q 66 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR q 66 " --> pdb=" O ARG q 74 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL q 80 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE q 60 " --> pdb=" O VAL q 80 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL q 61 " --> pdb=" O GLY q 12 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'q' and resid 30 through 32 removed outlier: 3.567A pdb=" N LYS q 31 " --> pdb=" O VAL q 40 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 's' and resid 32 through 33 Processing sheet with id=AI2, first strand: chain 'x' and resid 393 through 397 Processing sheet with id=AI3, first strand: chain 'x' and resid 435 through 437 removed outlier: 3.736A pdb=" N LYS x 435 " --> pdb=" O VAL x 432 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA x 430 " --> pdb=" O VAL x 437 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'x' and resid 598 through 599 removed outlier: 3.528A pdb=" N SER x 622 " --> pdb=" O PHE x 614 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'x' and resid 686 through 693 removed outlier: 3.518A pdb=" N SER x 690 " --> pdb=" O HIS x 702 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR x 666 " --> pdb=" O ILE x 726 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE x 726 " --> pdb=" O TYR x 666 " (cutoff:3.500A) 1339 hydrogen bonds defined for protein. 3690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2530 hydrogen bonds 4108 hydrogen bond angles 0 basepair planarities 1051 basepair parallelities 2347 stacking parallelities Total time for adding SS restraints: 179.00 Time building geometry restraints manager: 73.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.58: 149904 1.58 - 1.97: 9627 1.97 - 2.35: 5 2.35 - 2.73: 0 2.73 - 3.12: 1 Bond restraints: 159537 Sorted by residual: bond pdb=" CD GLN W 34 " pdb=" NE2 GLN W 34 " ideal model delta sigma weight residual 1.328 3.116 -1.788 2.10e-02 2.27e+03 7.25e+03 bond pdb=" C2 U A2120 " pdb=" N3 U A2120 " ideal model delta sigma weight residual 1.373 2.123 -0.750 2.00e-02 2.50e+03 1.41e+03 bond pdb=" N3 U A2120 " pdb=" C4 U A2120 " ideal model delta sigma weight residual 1.380 2.108 -0.728 2.00e-02 2.50e+03 1.33e+03 bond pdb=" N1 U A2120 " pdb=" C2 U A2120 " ideal model delta sigma weight residual 1.381 2.087 -0.706 2.00e-02 2.50e+03 1.25e+03 bond pdb=" N1 U A2120 " pdb=" C6 U A2120 " ideal model delta sigma weight residual 1.375 2.046 -0.671 2.00e-02 2.50e+03 1.12e+03 ... (remaining 159532 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.67: 25204 105.67 - 113.57: 99614 113.57 - 121.46: 74241 121.46 - 129.36: 36673 129.36 - 137.26: 3247 Bond angle restraints: 238979 Sorted by residual: angle pdb=" CG GLN W 34 " pdb=" CD GLN W 34 " pdb=" NE2 GLN W 34 " ideal model delta sigma weight residual 116.40 132.10 -15.70 1.50e+00 4.44e-01 1.10e+02 angle pdb=" CG GLN W 34 " pdb=" CD GLN W 34 " pdb=" OE1 GLN W 34 " ideal model delta sigma weight residual 120.80 102.35 18.45 2.00e+00 2.50e-01 8.51e+01 angle pdb=" CA ILE W 7 " pdb=" C ILE W 7 " pdb=" N THR W 8 " ideal model delta sigma weight residual 116.60 126.08 -9.48 1.45e+00 4.76e-01 4.27e+01 angle pdb=" C LEU S 38 " pdb=" N THR S 39 " pdb=" CA THR S 39 " ideal model delta sigma weight residual 121.80 136.58 -14.78 2.44e+00 1.68e-01 3.67e+01 angle pdb=" O4' U A2260 " pdb=" C1' U A2260 " pdb=" N1 U A2260 " ideal model delta sigma weight residual 108.50 117.54 -9.04 1.50e+00 4.44e-01 3.63e+01 ... (remaining 238974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 88835 35.92 - 71.84: 12019 71.84 - 107.77: 1463 107.77 - 143.69: 37 143.69 - 179.61: 70 Dihedral angle restraints: 102424 sinusoidal: 86355 harmonic: 16069 Sorted by residual: dihedral pdb=" CA ASN R 50 " pdb=" C ASN R 50 " pdb=" N PRO R 51 " pdb=" CA PRO R 51 " ideal model delta harmonic sigma weight residual 180.00 113.06 66.94 0 5.00e+00 4.00e-02 1.79e+02 dihedral pdb=" CA THR S 39 " pdb=" C THR S 39 " pdb=" N PRO S 40 " pdb=" CA PRO S 40 " ideal model delta harmonic sigma weight residual -180.00 -115.56 -64.44 0 5.00e+00 4.00e-02 1.66e+02 dihedral pdb=" CA LYS l 57 " pdb=" C LYS l 57 " pdb=" N PRO l 58 " pdb=" CA PRO l 58 " ideal model delta harmonic sigma weight residual -180.00 -117.25 -62.75 0 5.00e+00 4.00e-02 1.57e+02 ... (remaining 102421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 29147 0.093 - 0.187: 1309 0.187 - 0.280: 87 0.280 - 0.374: 34 0.374 - 0.467: 8 Chirality restraints: 30585 Sorted by residual: chirality pdb=" C3' A A2468 " pdb=" C4' A A2468 " pdb=" O3' A A2468 " pdb=" C2' A A2468 " both_signs ideal model delta sigma weight residual False -2.74 -2.28 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1' U A2260 " pdb=" O4' U A2260 " pdb=" C2' U A2260 " pdb=" N1 U A2260 " both_signs ideal model delta sigma weight residual False 2.47 2.03 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CB VAL W 6 " pdb=" CA VAL W 6 " pdb=" CG1 VAL W 6 " pdb=" CG2 VAL W 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 30582 not shown) Planarity restraints: 12519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR x 577 " -0.080 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO x 578 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO x 578 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO x 578 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 50 " -0.080 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO R 51 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO R 51 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO R 51 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA d 32 " 0.075 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO d 33 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO d 33 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO d 33 " 0.064 5.00e-02 4.00e+02 ... (remaining 12516 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 23372 2.75 - 3.29: 130209 3.29 - 3.83: 317708 3.83 - 4.36: 362720 4.36 - 4.90: 491051 Nonbonded interactions: 1325060 Sorted by model distance: nonbonded pdb=" O2' G A 818 " pdb=" O2' G A1394 " model vdw 2.213 2.440 nonbonded pdb=" O2' G A 512 " pdb=" O2' U A 730 " model vdw 2.219 2.440 nonbonded pdb=" O2' C A 737 " pdb=" OP1 G A 827 " model vdw 2.220 2.440 nonbonded pdb=" O2' C A1409 " pdb=" OG SER W 25 " model vdw 2.235 2.440 nonbonded pdb=" O2' U A 615 " pdb=" OP2 G A 617 " model vdw 2.241 2.440 ... (remaining 1325055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'u' and (resid 2 through 16 or resid 18 through 76)) selection = (chain 'w' and (resid 2 through 16 or resid 18 through 76)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 15.120 Check model and map are aligned: 1.630 Set scattering table: 1.010 Process input model: 454.430 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 480.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.788 159537 Z= 0.482 Angle : 0.894 19.995 238979 Z= 0.451 Chirality : 0.045 0.467 30585 Planarity : 0.006 0.122 12519 Dihedral : 24.379 179.610 92077 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.28 % Favored : 89.42 % Rotamer: Outliers : 0.32 % Allowed : 4.25 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 2.94 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.09), residues: 5546 helix: -3.93 (0.07), residues: 1561 sheet: -1.97 (0.17), residues: 823 loop : -2.83 (0.09), residues: 3162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP Q 61 HIS 0.023 0.003 HIS M 13 PHE 0.029 0.003 PHE C 257 TYR 0.036 0.003 TYR q 30 ARG 0.022 0.001 ARG q 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2747 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 2732 time to evaluate : 6.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ILE cc_start: 0.8422 (mt) cc_final: 0.8116 (mt) REVERT: C 98 ASP cc_start: 0.7706 (m-30) cc_final: 0.7291 (m-30) REVERT: C 141 VAL cc_start: 0.8824 (t) cc_final: 0.8298 (p) REVERT: C 198 GLU cc_start: 0.8003 (tt0) cc_final: 0.7438 (tt0) REVERT: C 259 THR cc_start: 0.9025 (p) cc_final: 0.8265 (t) REVERT: D 37 GLN cc_start: 0.8320 (tt0) cc_final: 0.7948 (tm-30) REVERT: D 54 ASP cc_start: 0.6446 (t70) cc_final: 0.6221 (t0) REVERT: D 60 LEU cc_start: 0.7996 (mt) cc_final: 0.7554 (tp) REVERT: D 100 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7314 (tm-30) REVERT: D 169 ILE cc_start: 0.7933 (mt) cc_final: 0.7686 (mt) REVERT: E 27 GLU cc_start: 0.7242 (pp20) cc_final: 0.6952 (tm-30) REVERT: E 29 ASN cc_start: 0.7262 (t160) cc_final: 0.6495 (m110) REVERT: E 39 MET cc_start: 0.7164 (tmt) cc_final: 0.6934 (tmt) REVERT: E 111 LYS cc_start: 0.8924 (mttt) cc_final: 0.8603 (mtpp) REVERT: E 160 ASN cc_start: 0.8831 (m-40) cc_final: 0.8536 (m-40) REVERT: E 189 HIS cc_start: 0.7988 (m-70) cc_final: 0.7546 (m170) REVERT: E 202 VAL cc_start: 0.9068 (t) cc_final: 0.8787 (t) REVERT: F 20 PHE cc_start: 0.8345 (m-80) cc_final: 0.7613 (m-80) REVERT: F 23 ASP cc_start: 0.8644 (m-30) cc_final: 0.8269 (m-30) REVERT: F 154 ILE cc_start: 0.8511 (mt) cc_final: 0.8145 (mt) REVERT: G 65 LEU cc_start: 0.8982 (mt) cc_final: 0.7920 (mp) REVERT: G 107 ASN cc_start: 0.8733 (m-40) cc_final: 0.8477 (m-40) REVERT: G 132 VAL cc_start: 0.9235 (t) cc_final: 0.9003 (p) REVERT: J 51 THR cc_start: 0.9138 (p) cc_final: 0.8839 (t) REVERT: K 1 MET cc_start: 0.7026 (mmm) cc_final: 0.6586 (mmm) REVERT: K 2 ILE cc_start: 0.8363 (mt) cc_final: 0.8105 (mm) REVERT: K 70 ARG cc_start: 0.6421 (tmt170) cc_final: 0.6182 (tmt170) REVERT: L 6 LEU cc_start: 0.9076 (mt) cc_final: 0.8697 (mp) REVERT: L 23 ILE cc_start: 0.7526 (pt) cc_final: 0.7303 (tp) REVERT: L 51 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6786 (mt-10) REVERT: L 57 LEU cc_start: 0.8915 (tt) cc_final: 0.8541 (tp) REVERT: L 58 PHE cc_start: 0.8269 (p90) cc_final: 0.7963 (p90) REVERT: L 112 LEU cc_start: 0.8747 (mt) cc_final: 0.8474 (mt) REVERT: M 35 GLN cc_start: 0.7762 (mt0) cc_final: 0.7548 (mt0) REVERT: M 46 GLN cc_start: 0.9299 (mt0) cc_final: 0.8597 (mt0) REVERT: M 103 LEU cc_start: 0.8926 (mt) cc_final: 0.8670 (mt) REVERT: M 124 LYS cc_start: 0.8839 (mmtm) cc_final: 0.8474 (mmmm) REVERT: M 131 PHE cc_start: 0.8022 (t80) cc_final: 0.7774 (t80) REVERT: N 20 LEU cc_start: 0.9057 (mt) cc_final: 0.8715 (mt) REVERT: N 59 ARG cc_start: 0.8307 (tpp80) cc_final: 0.7860 (tpp80) REVERT: N 76 ASN cc_start: 0.8452 (m-40) cc_final: 0.8218 (t0) REVERT: N 80 LEU cc_start: 0.9282 (tt) cc_final: 0.9026 (tp) REVERT: N 81 GLN cc_start: 0.8623 (mt0) cc_final: 0.7737 (mt0) REVERT: N 84 PHE cc_start: 0.8857 (m-80) cc_final: 0.8483 (m-80) REVERT: N 95 GLN cc_start: 0.8385 (mt0) cc_final: 0.8118 (mp10) REVERT: N 103 LYS cc_start: 0.8559 (mttp) cc_final: 0.8226 (mttt) REVERT: N 104 LEU cc_start: 0.8464 (mt) cc_final: 0.8263 (mt) REVERT: N 116 ILE cc_start: 0.8753 (mt) cc_final: 0.6789 (mt) REVERT: O 17 ARG cc_start: 0.8459 (ttm110) cc_final: 0.7959 (mtp180) REVERT: O 44 ILE cc_start: 0.9070 (mt) cc_final: 0.8013 (mp) REVERT: O 45 ILE cc_start: 0.8738 (mt) cc_final: 0.8404 (mp) REVERT: O 52 THR cc_start: 0.9153 (p) cc_final: 0.8950 (p) REVERT: O 75 THR cc_start: 0.9021 (m) cc_final: 0.8812 (p) REVERT: O 80 LEU cc_start: 0.9415 (mt) cc_final: 0.9092 (tt) REVERT: O 101 LEU cc_start: 0.8545 (mt) cc_final: 0.8324 (mt) REVERT: O 109 LEU cc_start: 0.9286 (mt) cc_final: 0.9067 (mt) REVERT: P 3 LYS cc_start: 0.7495 (tttt) cc_final: 0.7251 (tptt) REVERT: P 4 LEU cc_start: 0.8698 (tt) cc_final: 0.8489 (tt) REVERT: P 50 ARG cc_start: 0.7548 (ttm170) cc_final: 0.7146 (ttm-80) REVERT: P 51 ARG cc_start: 0.7883 (ppp-140) cc_final: 0.7646 (ttp-170) REVERT: P 63 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8006 (tttt) REVERT: P 89 TYR cc_start: 0.8651 (m-80) cc_final: 0.8420 (m-10) REVERT: P 101 ARG cc_start: 0.7339 (mtt180) cc_final: 0.7068 (mtt180) REVERT: Q 27 SER cc_start: 0.8970 (t) cc_final: 0.8629 (t) REVERT: Q 36 ASN cc_start: 0.8005 (t0) cc_final: 0.7773 (t0) REVERT: Q 45 TYR cc_start: 0.8478 (m-10) cc_final: 0.8067 (m-10) REVERT: Q 48 ARG cc_start: 0.8475 (ppt-90) cc_final: 0.8252 (ttp-170) REVERT: Q 61 TRP cc_start: 0.8924 (m-10) cc_final: 0.8329 (m-90) REVERT: Q 94 MET cc_start: 0.7124 (ttt) cc_final: 0.6397 (ttt) REVERT: Q 101 ASN cc_start: 0.6465 (m-40) cc_final: 0.3605 (p0) REVERT: Q 102 ASP cc_start: 0.8484 (m-30) cc_final: 0.8158 (t0) REVERT: R 2 TYR cc_start: 0.7360 (p90) cc_final: 0.6965 (p90) REVERT: R 13 LYS cc_start: 0.8497 (tttm) cc_final: 0.8283 (ttmt) REVERT: S 33 VAL cc_start: 0.8786 (t) cc_final: 0.8487 (t) REVERT: S 62 TYR cc_start: 0.7428 (m-80) cc_final: 0.7075 (m-80) REVERT: S 70 VAL cc_start: 0.8570 (t) cc_final: 0.8229 (p) REVERT: S 106 VAL cc_start: 0.8912 (t) cc_final: 0.8005 (t) REVERT: T 13 ILE cc_start: 0.9212 (mp) cc_final: 0.8857 (tp) REVERT: T 30 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8198 (t) REVERT: T 46 ILE cc_start: 0.7968 (mt) cc_final: 0.7502 (mt) REVERT: T 57 MET cc_start: 0.7157 (mtp) cc_final: 0.6301 (mtp) REVERT: T 64 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7860 (mmtt) REVERT: T 69 TYR cc_start: 0.6639 (m-80) cc_final: 0.5705 (m-80) REVERT: T 74 SER cc_start: 0.8664 (p) cc_final: 0.8444 (t) REVERT: T 78 LYS cc_start: 0.8765 (ptmt) cc_final: 0.8375 (ptmt) REVERT: U 12 ILE cc_start: 0.9122 (mt) cc_final: 0.8858 (tt) REVERT: U 64 HIS cc_start: 0.8497 (t70) cc_final: 0.8134 (t70) REVERT: V 19 LYS cc_start: 0.8263 (tppp) cc_final: 0.8047 (tppt) REVERT: V 20 ASN cc_start: 0.8947 (m-40) cc_final: 0.8706 (m-40) REVERT: V 22 ARG cc_start: 0.7793 (pmt170) cc_final: 0.6687 (pmt170) REVERT: V 90 TYR cc_start: 0.8319 (m-80) cc_final: 0.7448 (m-80) REVERT: W 47 VAL cc_start: 0.4980 (OUTLIER) cc_final: 0.4600 (m) REVERT: X 21 LEU cc_start: 0.9555 (mp) cc_final: 0.9322 (pp) REVERT: X 56 VAL cc_start: 0.9315 (t) cc_final: 0.8981 (t) REVERT: X 57 ILE cc_start: 0.9261 (mt) cc_final: 0.9048 (mm) REVERT: Y 44 ARG cc_start: 0.8752 (tpp80) cc_final: 0.8414 (tpp80) REVERT: 1 10 LYS cc_start: 0.6394 (mtmt) cc_final: 0.6153 (mtmt) REVERT: 2 17 TYR cc_start: 0.6776 (m-80) cc_final: 0.6532 (m-80) REVERT: 2 25 ASN cc_start: 0.8797 (m-40) cc_final: 0.8476 (m110) REVERT: 2 29 ARG cc_start: 0.8985 (ttm170) cc_final: 0.7972 (mtt-85) REVERT: 2 30 VAL cc_start: 0.9028 (p) cc_final: 0.8614 (p) REVERT: 2 44 LEU cc_start: 0.8950 (tm) cc_final: 0.8210 (tm) REVERT: 2 47 GLU cc_start: 0.8162 (tt0) cc_final: 0.7540 (tm-30) REVERT: 2 48 THR cc_start: 0.8617 (p) cc_final: 0.8149 (p) REVERT: 3 1 MET cc_start: 0.4617 (mmm) cc_final: 0.4349 (mmp) REVERT: 3 14 LYS cc_start: 0.7501 (ttmm) cc_final: 0.7210 (ttmm) REVERT: 4 25 SER cc_start: 0.8115 (m) cc_final: 0.7759 (t) REVERT: 4 37 SER cc_start: 0.8970 (p) cc_final: 0.8502 (p) REVERT: 4 39 LYS cc_start: 0.8905 (ttpp) cc_final: 0.8493 (ttmm) REVERT: 4 41 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8658 (mtmm) REVERT: 4 56 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8290 (ttmm) REVERT: 4 62 LEU cc_start: 0.8456 (pp) cc_final: 0.8058 (pp) REVERT: 5 2 LYS cc_start: 0.7437 (mttm) cc_final: 0.6797 (mttm) REVERT: 5 4 ARG cc_start: 0.8285 (ptp-170) cc_final: 0.8049 (ptm160) REVERT: 5 19 ARG cc_start: 0.8044 (ttm170) cc_final: 0.6887 (ttm170) REVERT: Z 20 ASN cc_start: 0.7782 (m-40) cc_final: 0.6995 (m110) REVERT: Z 22 PHE cc_start: 0.8171 (t80) cc_final: 0.7946 (t80) REVERT: Z 31 VAL cc_start: 0.8566 (t) cc_final: 0.7637 (t) REVERT: Z 33 VAL cc_start: 0.9147 (t) cc_final: 0.8936 (t) REVERT: Z 35 ILE cc_start: 0.8774 (mt) cc_final: 0.8392 (mp) REVERT: b 26 LYS cc_start: 0.8585 (mmtm) cc_final: 0.7885 (mmtp) REVERT: b 40 ILE cc_start: 0.8976 (mt) cc_final: 0.8713 (mt) REVERT: b 86 ARG cc_start: 0.8432 (tmm-80) cc_final: 0.8180 (ttp-170) REVERT: b 96 TRP cc_start: 0.8008 (t60) cc_final: 0.7373 (t60) REVERT: b 104 PHE cc_start: 0.7611 (t80) cc_final: 0.6131 (t80) REVERT: b 114 LEU cc_start: 0.8868 (tp) cc_final: 0.8615 (tt) REVERT: b 171 ILE cc_start: 0.8034 (mp) cc_final: 0.7625 (mp) REVERT: c 23 TYR cc_start: 0.8184 (t80) cc_final: 0.7811 (t80) REVERT: c 36 LEU cc_start: 0.9601 (mt) cc_final: 0.8909 (mp) REVERT: c 43 SER cc_start: 0.9475 (t) cc_final: 0.9216 (p) REVERT: c 84 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7457 (tp30) REVERT: c 104 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7301 (tm-30) REVERT: c 118 ASN cc_start: 0.9428 (t0) cc_final: 0.9065 (t0) REVERT: c 198 LYS cc_start: 0.8780 (mttt) cc_final: 0.8515 (mttt) REVERT: d 10 LYS cc_start: 0.7474 (tttt) cc_final: 0.7266 (tttt) REVERT: d 50 GLN cc_start: 0.9399 (mt0) cc_final: 0.8613 (mm110) REVERT: d 51 LEU cc_start: 0.8777 (mt) cc_final: 0.8477 (tp) REVERT: d 52 GLN cc_start: 0.8966 (mt0) cc_final: 0.8653 (mt0) REVERT: d 59 HIS cc_start: 0.8752 (m-70) cc_final: 0.8391 (m-70) REVERT: d 71 LEU cc_start: 0.8753 (mt) cc_final: 0.8137 (mt) REVERT: d 84 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8770 (mp0) REVERT: d 120 LEU cc_start: 0.8087 (mp) cc_final: 0.7377 (pp) REVERT: d 151 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8679 (mp) REVERT: d 198 TYR cc_start: 0.8331 (m-80) cc_final: 0.7632 (m-10) REVERT: e 20 ARG cc_start: 0.8063 (ptm160) cc_final: 0.7600 (ptp-170) REVERT: e 30 ARG cc_start: 0.7142 (mmt-90) cc_final: 0.6891 (mpt180) REVERT: e 43 ASN cc_start: 0.8507 (m-40) cc_final: 0.8118 (t0) REVERT: e 52 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8296 (mtpt) REVERT: e 55 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6406 (mp0) REVERT: e 65 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7401 (tt0) REVERT: e 88 ARG cc_start: 0.7458 (mtt-85) cc_final: 0.7253 (mmt180) REVERT: e 95 LEU cc_start: 0.7950 (pt) cc_final: 0.7415 (pt) REVERT: e 141 LEU cc_start: 0.9218 (mt) cc_final: 0.8984 (pt) REVERT: e 147 LEU cc_start: 0.8785 (mt) cc_final: 0.8372 (mm) REVERT: e 165 LEU cc_start: 0.8967 (tp) cc_final: 0.8589 (pp) REVERT: f 5 GLU cc_start: 0.8159 (tt0) cc_final: 0.7547 (tm-30) REVERT: f 60 TYR cc_start: 0.8005 (m-80) cc_final: 0.7692 (m-80) REVERT: f 62 ILE cc_start: 0.8468 (mt) cc_final: 0.6717 (mt) REVERT: f 78 LEU cc_start: 0.9370 (mt) cc_final: 0.9107 (mt) REVERT: g 28 ASN cc_start: 0.8610 (m-40) cc_final: 0.8244 (m-40) REVERT: g 29 LYS cc_start: 0.9150 (tppt) cc_final: 0.8936 (tppp) REVERT: g 31 MET cc_start: 0.9012 (ttm) cc_final: 0.8081 (ttt) REVERT: g 48 ASP cc_start: 0.8727 (t0) cc_final: 0.8401 (t0) REVERT: g 49 ILE cc_start: 0.9337 (mt) cc_final: 0.8745 (mt) REVERT: g 61 VAL cc_start: 0.8770 (t) cc_final: 0.8266 (t) REVERT: g 113 GLU cc_start: 0.7808 (mt-10) cc_final: 0.5734 (mp0) REVERT: g 117 GLU cc_start: 0.8007 (tt0) cc_final: 0.6946 (tt0) REVERT: g 118 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8709 (tm-30) REVERT: g 130 ASN cc_start: 0.8414 (p0) cc_final: 0.8132 (p0) REVERT: h 10 MET cc_start: 0.8295 (ptm) cc_final: 0.7649 (ttp) REVERT: h 14 ILE cc_start: 0.9284 (mt) cc_final: 0.9060 (mm) REVERT: h 24 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8293 (tppt) REVERT: h 25 LEU cc_start: 0.7958 (mt) cc_final: 0.7385 (tp) REVERT: h 27 ILE cc_start: 0.8272 (mt) cc_final: 0.7668 (mm) REVERT: h 30 SER cc_start: 0.7958 (p) cc_final: 0.7223 (t) REVERT: h 51 PHE cc_start: 0.6918 (m-80) cc_final: 0.6222 (m-10) REVERT: h 86 ARG cc_start: 0.8125 (mmt180) cc_final: 0.7846 (mmt180) REVERT: h 90 LYS cc_start: 0.7810 (mttt) cc_final: 0.7423 (mmtm) REVERT: h 98 LEU cc_start: 0.9270 (mt) cc_final: 0.8482 (mm) REVERT: h 101 LEU cc_start: 0.8972 (tp) cc_final: 0.8680 (tt) REVERT: h 108 THR cc_start: 0.8807 (p) cc_final: 0.8593 (p) REVERT: h 112 VAL cc_start: 0.8907 (t) cc_final: 0.8556 (m) REVERT: h 126 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7366 (mm-30) REVERT: i 13 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8953 (ttmt) REVERT: i 79 ILE cc_start: 0.9455 (mt) cc_final: 0.9187 (mt) REVERT: i 81 HIS cc_start: 0.8060 (t70) cc_final: 0.7850 (t-90) REVERT: j 53 ARG cc_start: 0.8324 (ttm170) cc_final: 0.6830 (ttm170) REVERT: j 61 SER cc_start: 0.8880 (p) cc_final: 0.8532 (p) REVERT: j 63 GLU cc_start: 0.8154 (tt0) cc_final: 0.7781 (tt0) REVERT: j 90 LEU cc_start: 0.8982 (mt) cc_final: 0.8693 (mt) REVERT: k 22 ILE cc_start: 0.9268 (pt) cc_final: 0.8787 (pt) REVERT: k 24 HIS cc_start: 0.8342 (m-70) cc_final: 0.8046 (m170) REVERT: k 37 THR cc_start: 0.9316 (p) cc_final: 0.8896 (t) REVERT: k 88 VAL cc_start: 0.8697 (t) cc_final: 0.7964 (m) REVERT: k 107 LEU cc_start: 0.8450 (mt) cc_final: 0.8218 (mm) REVERT: k 114 ASP cc_start: 0.8155 (m-30) cc_final: 0.7886 (m-30) REVERT: l 21 SER cc_start: 0.8591 (p) cc_final: 0.8344 (p) REVERT: l 72 ASN cc_start: 0.8323 (p0) cc_final: 0.8106 (p0) REVERT: l 111 VAL cc_start: 0.8965 (t) cc_final: 0.8598 (p) REVERT: m 23 PHE cc_start: 0.8278 (t80) cc_final: 0.7677 (t80) REVERT: m 29 THR cc_start: 0.9538 (p) cc_final: 0.9312 (p) REVERT: m 48 LEU cc_start: 0.8775 (mt) cc_final: 0.8362 (tp) REVERT: m 53 LEU cc_start: 0.8284 (tt) cc_final: 0.7967 (tp) REVERT: m 81 ILE cc_start: 0.8886 (mt) cc_final: 0.8616 (tt) REVERT: m 83 ILE cc_start: 0.8539 (pt) cc_final: 0.8220 (pt) REVERT: m 87 ARG cc_start: 0.8868 (ttp80) cc_final: 0.8425 (ttt90) REVERT: m 89 ILE cc_start: 0.9274 (mt) cc_final: 0.9012 (mm) REVERT: n 4 LYS cc_start: 0.8761 (mttt) cc_final: 0.8376 (mttt) REVERT: n 6 MET cc_start: 0.8608 (mmm) cc_final: 0.8196 (mmt) REVERT: n 17 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8147 (tptp) REVERT: n 19 GLN cc_start: 0.8563 (mt0) cc_final: 0.8082 (mt0) REVERT: n 39 LEU cc_start: 0.9367 (mt) cc_final: 0.8727 (tp) REVERT: n 42 ILE cc_start: 0.9244 (mt) cc_final: 0.8929 (tp) REVERT: n 44 PHE cc_start: 0.9038 (t80) cc_final: 0.8727 (t80) REVERT: o 7 ARG cc_start: 0.8342 (tpp80) cc_final: 0.8106 (tpt90) REVERT: o 11 LEU cc_start: 0.8957 (mt) cc_final: 0.8511 (mt) REVERT: o 17 THR cc_start: 0.9191 (p) cc_final: 0.8772 (p) REVERT: o 62 LYS cc_start: 0.8645 (mttt) cc_final: 0.7977 (mmmt) REVERT: p 49 VAL cc_start: 0.7802 (t) cc_final: 0.7507 (t) REVERT: p 59 TRP cc_start: 0.8828 (m100) cc_final: 0.8615 (m100) REVERT: p 65 LYS cc_start: 0.8930 (mttt) cc_final: 0.8685 (mttm) REVERT: p 77 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8460 (tm-30) REVERT: p 79 ILE cc_start: 0.8665 (mp) cc_final: 0.8030 (mp) REVERT: q 10 TYR cc_start: 0.8110 (m-80) cc_final: 0.7522 (m-80) REVERT: q 19 MET cc_start: 0.7730 (mpp) cc_final: 0.7186 (mmp) REVERT: q 25 VAL cc_start: 0.8788 (t) cc_final: 0.8583 (m) REVERT: q 32 LYS cc_start: 0.7415 (pptt) cc_final: 0.6990 (mtmm) REVERT: q 40 VAL cc_start: 0.8691 (t) cc_final: 0.8457 (t) REVERT: q 41 LYS cc_start: 0.8455 (pttt) cc_final: 0.7846 (ptpp) REVERT: q 63 ILE cc_start: 0.8720 (pt) cc_final: 0.8251 (pt) REVERT: q 65 GLU cc_start: 0.8102 (pp20) cc_final: 0.7772 (pp20) REVERT: q 70 SER cc_start: 0.6863 (p) cc_final: 0.6648 (m) REVERT: q 75 PHE cc_start: 0.8556 (m-80) cc_final: 0.8264 (m-80) REVERT: r 33 LEU cc_start: 0.8791 (tt) cc_final: 0.8279 (tp) REVERT: r 45 LEU cc_start: 0.9052 (mt) cc_final: 0.8602 (mt) REVERT: t 13 THR cc_start: 0.8857 (p) cc_final: 0.8420 (p) REVERT: t 21 ASN cc_start: 0.7278 (t0) cc_final: 0.7047 (t0) REVERT: t 25 LYS cc_start: 0.8554 (mttt) cc_final: 0.8076 (mttm) REVERT: t 32 ILE cc_start: 0.9634 (mt) cc_final: 0.9315 (mm) REVERT: t 41 ASN cc_start: 0.8462 (t0) cc_final: 0.8144 (t0) REVERT: t 42 ASN cc_start: 0.8515 (m-40) cc_final: 0.8247 (m-40) REVERT: t 60 LYS cc_start: 0.8816 (mttt) cc_final: 0.7579 (ttmm) REVERT: t 71 THR cc_start: 0.8621 (p) cc_final: 0.8181 (p) REVERT: x 467 LEU cc_start: 0.8054 (mt) cc_final: 0.7786 (mt) REVERT: x 532 MET cc_start: 0.4164 (mtm) cc_final: 0.3201 (mmt) REVERT: x 595 LEU cc_start: 0.9355 (mt) cc_final: 0.8982 (mt) REVERT: x 658 ASN cc_start: 0.8362 (m-40) cc_final: 0.7969 (m110) REVERT: x 663 ILE cc_start: 0.8081 (mt) cc_final: 0.6549 (mp) outliers start: 15 outliers final: 3 residues processed: 2739 average time/residue: 1.4055 time to fit residues: 6454.7202 Evaluate side-chains 1945 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1939 time to evaluate : 6.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 857 optimal weight: 20.0000 chunk 770 optimal weight: 0.0770 chunk 427 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 519 optimal weight: 20.0000 chunk 411 optimal weight: 0.7980 chunk 796 optimal weight: 20.0000 chunk 308 optimal weight: 9.9990 chunk 484 optimal weight: 5.9990 chunk 592 optimal weight: 10.0000 chunk 922 optimal weight: 0.2980 overall best weight: 3.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN C 95 ASN C 163 GLN C 177 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 50 GLN D 62 ASN D 172 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN J 96 ASN K 4 GLN L 38 GLN L 83 ASN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN ** N 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN P 29 HIS Q 36 ASN ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 88 HIS U 64 HIS ** W 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 HIS 1 40 HIS 2 4 ASN ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 40 GLN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 77 GLN ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 122 GLN d 96 ASN d 116 HIS d 147 ASN e 45 HIS e 83 HIS ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS h 18 ASN h 57 GLN i 68 HIS i 75 GLN ** k 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 59 ASN m 32 GLN o 42 HIS o 46 HIS ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 20 HIS t 68 HIS ** x 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 528 ASN x 545 GLN x 634 ASN x 722 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 159537 Z= 0.225 Angle : 0.705 17.140 238979 Z= 0.359 Chirality : 0.039 0.377 30585 Planarity : 0.006 0.110 12519 Dihedral : 25.313 179.715 80645 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.43 % Favored : 90.30 % Rotamer: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.96 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.10), residues: 5546 helix: -2.17 (0.11), residues: 1639 sheet: -1.54 (0.17), residues: 838 loop : -2.45 (0.10), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP W 29 HIS 0.007 0.002 HIS Q 81 PHE 0.025 0.002 PHE Z 59 TYR 0.022 0.002 TYR t 75 ARG 0.038 0.001 ARG d 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2259 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2252 time to evaluate : 6.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ILE cc_start: 0.9404 (mp) cc_final: 0.9075 (mp) REVERT: C 141 VAL cc_start: 0.8901 (t) cc_final: 0.8646 (p) REVERT: C 247 MET cc_start: 0.7784 (mtm) cc_final: 0.7503 (mtt) REVERT: D 14 GLN cc_start: 0.8217 (tt0) cc_final: 0.7998 (tt0) REVERT: D 37 GLN cc_start: 0.8291 (tt0) cc_final: 0.7973 (tm-30) REVERT: D 54 ASP cc_start: 0.6490 (t70) cc_final: 0.6235 (t0) REVERT: D 82 GLU cc_start: 0.6337 (tt0) cc_final: 0.6112 (tt0) REVERT: D 100 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7454 (tm-30) REVERT: D 154 VAL cc_start: 0.8753 (t) cc_final: 0.8491 (p) REVERT: D 169 ILE cc_start: 0.8053 (mt) cc_final: 0.7705 (mt) REVERT: D 185 LEU cc_start: 0.9088 (mt) cc_final: 0.8788 (mt) REVERT: D 186 LEU cc_start: 0.9156 (mt) cc_final: 0.8884 (mt) REVERT: D 199 LEU cc_start: 0.8879 (tt) cc_final: 0.7925 (pt) REVERT: E 24 PHE cc_start: 0.8659 (m-80) cc_final: 0.8453 (m-80) REVERT: E 30 GLU cc_start: 0.7054 (mm-30) cc_final: 0.4402 (tp30) REVERT: E 38 LEU cc_start: 0.9306 (mt) cc_final: 0.8931 (tt) REVERT: E 111 LYS cc_start: 0.9030 (mttt) cc_final: 0.8664 (mtpp) REVERT: E 185 ASP cc_start: 0.8571 (m-30) cc_final: 0.7860 (m-30) REVERT: E 189 HIS cc_start: 0.8011 (m-70) cc_final: 0.6884 (m-70) REVERT: F 20 PHE cc_start: 0.7790 (m-80) cc_final: 0.6786 (m-10) REVERT: F 135 GLN cc_start: 0.7825 (pt0) cc_final: 0.7493 (pt0) REVERT: F 138 PHE cc_start: 0.6877 (p90) cc_final: 0.6459 (p90) REVERT: G 38 PHE cc_start: 0.7503 (m-80) cc_final: 0.7109 (m-80) REVERT: J 16 TRP cc_start: 0.8592 (m100) cc_final: 0.8225 (m100) REVERT: J 119 MET cc_start: 0.8077 (mtm) cc_final: 0.7842 (mtm) REVERT: K 1 MET cc_start: 0.7205 (mmm) cc_final: 0.6833 (mmm) REVERT: K 2 ILE cc_start: 0.8344 (mt) cc_final: 0.8094 (mm) REVERT: K 5 GLU cc_start: 0.8537 (mp0) cc_final: 0.7916 (mp0) REVERT: K 54 LYS cc_start: 0.7611 (tttp) cc_final: 0.7047 (ttpt) REVERT: K 64 ARG cc_start: 0.6873 (ptt-90) cc_final: 0.6500 (ptt-90) REVERT: L 23 ILE cc_start: 0.7638 (pt) cc_final: 0.7212 (tp) REVERT: L 50 PHE cc_start: 0.8597 (t80) cc_final: 0.8284 (t80) REVERT: M 1 MET cc_start: 0.6775 (tpt) cc_final: 0.6383 (tpt) REVERT: M 3 LEU cc_start: 0.8893 (mm) cc_final: 0.8680 (mm) REVERT: M 25 THR cc_start: 0.8975 (p) cc_final: 0.8445 (p) REVERT: M 41 TRP cc_start: 0.8486 (m-10) cc_final: 0.8000 (m-10) REVERT: M 103 LEU cc_start: 0.8942 (mt) cc_final: 0.8685 (mm) REVERT: M 124 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8729 (mmmt) REVERT: M 128 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8057 (mtpt) REVERT: N 20 LEU cc_start: 0.9002 (mt) cc_final: 0.8690 (mm) REVERT: N 38 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8539 (mtpp) REVERT: N 49 THR cc_start: 0.8897 (p) cc_final: 0.8622 (p) REVERT: N 76 ASN cc_start: 0.8503 (m-40) cc_final: 0.8267 (t0) REVERT: N 81 GLN cc_start: 0.8830 (mt0) cc_final: 0.8249 (mt0) REVERT: N 82 LYS cc_start: 0.8871 (tttm) cc_final: 0.8095 (tttt) REVERT: N 95 GLN cc_start: 0.8366 (mt0) cc_final: 0.8068 (mp10) REVERT: O 11 ARG cc_start: 0.8396 (tmm-80) cc_final: 0.7734 (ttp80) REVERT: O 17 ARG cc_start: 0.8478 (ttm110) cc_final: 0.7688 (mtp180) REVERT: O 38 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8530 (mmmm) REVERT: O 52 THR cc_start: 0.8817 (p) cc_final: 0.8609 (p) REVERT: O 63 LEU cc_start: 0.9475 (pp) cc_final: 0.9269 (pp) REVERT: O 118 LEU cc_start: 0.8948 (mm) cc_final: 0.8691 (mm) REVERT: P 3 LYS cc_start: 0.7340 (tttt) cc_final: 0.7117 (tppt) REVERT: P 63 LYS cc_start: 0.8403 (ttpt) cc_final: 0.8100 (tttt) REVERT: P 84 ILE cc_start: 0.9349 (mp) cc_final: 0.9141 (mm) REVERT: Q 45 TYR cc_start: 0.8472 (m-10) cc_final: 0.7772 (m-10) REVERT: Q 52 GLN cc_start: 0.7892 (mt0) cc_final: 0.7671 (mm110) REVERT: Q 56 ASP cc_start: 0.7561 (t70) cc_final: 0.7304 (t70) REVERT: Q 80 MET cc_start: 0.8560 (mmm) cc_final: 0.8059 (tpp) REVERT: R 35 PHE cc_start: 0.8381 (m-80) cc_final: 0.7954 (m-10) REVERT: R 67 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7525 (mmm-85) REVERT: R 89 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7537 (mmm-85) REVERT: R 92 TYR cc_start: 0.8075 (p90) cc_final: 0.7655 (p90) REVERT: S 62 TYR cc_start: 0.7456 (m-80) cc_final: 0.7039 (m-80) REVERT: S 70 VAL cc_start: 0.8641 (t) cc_final: 0.8427 (p) REVERT: S 84 ARG cc_start: 0.6305 (mpt180) cc_final: 0.5828 (mpt180) REVERT: S 96 ILE cc_start: 0.7692 (mm) cc_final: 0.7386 (tt) REVERT: S 106 VAL cc_start: 0.8522 (t) cc_final: 0.7440 (t) REVERT: T 13 ILE cc_start: 0.9184 (mp) cc_final: 0.8752 (tp) REVERT: T 21 MET cc_start: 0.8700 (mtm) cc_final: 0.8210 (mtt) REVERT: T 28 PHE cc_start: 0.7589 (m-80) cc_final: 0.6956 (m-80) REVERT: T 46 ILE cc_start: 0.8136 (mt) cc_final: 0.7549 (mt) REVERT: T 57 MET cc_start: 0.7240 (mtp) cc_final: 0.6440 (mtt) REVERT: T 74 SER cc_start: 0.8772 (p) cc_final: 0.8462 (t) REVERT: T 78 LYS cc_start: 0.8660 (ptmt) cc_final: 0.8250 (pttm) REVERT: U 12 ILE cc_start: 0.9286 (mt) cc_final: 0.8914 (tt) REVERT: U 16 ASP cc_start: 0.7911 (t0) cc_final: 0.7702 (t0) REVERT: U 56 ILE cc_start: 0.8530 (mm) cc_final: 0.8175 (tp) REVERT: U 64 HIS cc_start: 0.8569 (t-90) cc_final: 0.8084 (t70) REVERT: U 99 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8160 (mm-40) REVERT: V 22 ARG cc_start: 0.7111 (pmt170) cc_final: 0.6846 (ptt-90) REVERT: V 46 TYR cc_start: 0.7896 (t80) cc_final: 0.7648 (t80) REVERT: X 21 LEU cc_start: 0.9619 (mp) cc_final: 0.9399 (pp) REVERT: X 28 LEU cc_start: 0.9064 (mm) cc_final: 0.8788 (tp) REVERT: X 37 LEU cc_start: 0.8308 (tt) cc_final: 0.8072 (tt) REVERT: X 43 ILE cc_start: 0.9290 (mp) cc_final: 0.8795 (mp) REVERT: X 53 MET cc_start: 0.8846 (ptp) cc_final: 0.7885 (ptm) REVERT: X 56 VAL cc_start: 0.9519 (t) cc_final: 0.8493 (t) REVERT: 2 25 ASN cc_start: 0.8766 (m-40) cc_final: 0.8499 (m110) REVERT: 2 29 ARG cc_start: 0.8681 (ttm170) cc_final: 0.8347 (mtp85) REVERT: 2 30 VAL cc_start: 0.9033 (p) cc_final: 0.8605 (p) REVERT: 2 48 THR cc_start: 0.8598 (p) cc_final: 0.7957 (p) REVERT: 3 1 MET cc_start: 0.5358 (mmm) cc_final: 0.4803 (mmp) REVERT: 3 14 LYS cc_start: 0.7794 (ttmm) cc_final: 0.7493 (ttmm) REVERT: 4 39 LYS cc_start: 0.8994 (ttpp) cc_final: 0.8715 (ttmm) REVERT: 4 56 LYS cc_start: 0.8992 (ttpp) cc_final: 0.8340 (ttmm) REVERT: 4 62 LEU cc_start: 0.8340 (pp) cc_final: 0.8091 (pp) REVERT: 5 4 ARG cc_start: 0.8101 (ptp-170) cc_final: 0.7882 (ptm160) REVERT: Z 10 LYS cc_start: 0.8402 (ptpt) cc_final: 0.8136 (mtmm) REVERT: b 26 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8678 (mmtp) REVERT: b 45 LYS cc_start: 0.9388 (mtmt) cc_final: 0.9083 (mtmt) REVERT: b 96 TRP cc_start: 0.7731 (t60) cc_final: 0.7453 (t60) REVERT: b 104 PHE cc_start: 0.7524 (t80) cc_final: 0.6772 (t80) REVERT: b 139 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8238 (mtpt) REVERT: b 178 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7838 (tptp) REVERT: c 33 HIS cc_start: 0.8377 (m90) cc_final: 0.7744 (m90) REVERT: c 41 TYR cc_start: 0.8242 (t80) cc_final: 0.7613 (t80) REVERT: c 88 LYS cc_start: 0.9292 (ptpp) cc_final: 0.9066 (pttm) REVERT: d 47 TYR cc_start: 0.7547 (t80) cc_final: 0.7230 (t80) REVERT: d 50 GLN cc_start: 0.9296 (mt0) cc_final: 0.8577 (mm-40) REVERT: d 59 HIS cc_start: 0.8612 (m-70) cc_final: 0.7842 (m-70) REVERT: d 66 ARG cc_start: 0.8558 (mmt90) cc_final: 0.8146 (tpp80) REVERT: d 87 MET cc_start: 0.8683 (mtp) cc_final: 0.8441 (mtp) REVERT: d 198 TYR cc_start: 0.7986 (m-80) cc_final: 0.7429 (m-10) REVERT: e 26 LYS cc_start: 0.7780 (tptt) cc_final: 0.7559 (ttpt) REVERT: e 88 ARG cc_start: 0.7528 (mtt-85) cc_final: 0.7136 (mmt180) REVERT: e 123 ILE cc_start: 0.8967 (mp) cc_final: 0.8664 (mp) REVERT: e 141 LEU cc_start: 0.9134 (mt) cc_final: 0.8805 (tt) REVERT: e 147 LEU cc_start: 0.8975 (mt) cc_final: 0.8719 (mm) REVERT: e 152 ASP cc_start: 0.8866 (m-30) cc_final: 0.8499 (m-30) REVERT: e 165 LEU cc_start: 0.8900 (tp) cc_final: 0.8475 (pp) REVERT: f 16 GLU cc_start: 0.8629 (mp0) cc_final: 0.8088 (mp0) REVERT: f 60 TYR cc_start: 0.8265 (m-80) cc_final: 0.7805 (m-80) REVERT: f 62 ILE cc_start: 0.8418 (mt) cc_final: 0.8056 (mt) REVERT: f 91 VAL cc_start: 0.8509 (t) cc_final: 0.8187 (t) REVERT: g 21 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7943 (mmpt) REVERT: g 28 ASN cc_start: 0.8695 (m-40) cc_final: 0.8298 (m-40) REVERT: g 31 MET cc_start: 0.9119 (ttm) cc_final: 0.8145 (ttt) REVERT: g 45 LYS cc_start: 0.9160 (tppt) cc_final: 0.8609 (tppt) REVERT: g 49 ILE cc_start: 0.9268 (mt) cc_final: 0.8869 (mt) REVERT: g 113 GLU cc_start: 0.7635 (mt-10) cc_final: 0.6335 (mm-30) REVERT: g 116 MET cc_start: 0.8537 (tpp) cc_final: 0.8302 (tpp) REVERT: g 118 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8467 (tm-30) REVERT: g 122 ASN cc_start: 0.9010 (m-40) cc_final: 0.8337 (m110) REVERT: g 130 ASN cc_start: 0.8749 (p0) cc_final: 0.8332 (p0) REVERT: g 140 ASP cc_start: 0.9478 (m-30) cc_final: 0.9245 (m-30) REVERT: g 149 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8725 (mtpp) REVERT: h 10 MET cc_start: 0.8637 (ptm) cc_final: 0.8148 (ttp) REVERT: h 25 LEU cc_start: 0.8204 (mt) cc_final: 0.7664 (mt) REVERT: h 27 ILE cc_start: 0.8191 (mt) cc_final: 0.7549 (mm) REVERT: h 30 SER cc_start: 0.7612 (p) cc_final: 0.7258 (t) REVERT: h 41 LYS cc_start: 0.8919 (tptm) cc_final: 0.8605 (mmmm) REVERT: h 80 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7542 (mp) REVERT: h 98 LEU cc_start: 0.9069 (mt) cc_final: 0.8591 (mm) REVERT: h 112 VAL cc_start: 0.9012 (t) cc_final: 0.8684 (m) REVERT: i 13 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8859 (ttmt) REVERT: i 19 VAL cc_start: 0.8361 (t) cc_final: 0.8105 (p) REVERT: i 25 GLU cc_start: 0.6685 (pp20) cc_final: 0.6347 (pp20) REVERT: i 28 ILE cc_start: 0.9082 (mm) cc_final: 0.8805 (mm) REVERT: i 46 GLU cc_start: 0.8424 (pt0) cc_final: 0.8180 (pt0) REVERT: i 81 HIS cc_start: 0.8110 (t70) cc_final: 0.7697 (t-90) REVERT: i 115 LYS cc_start: 0.7115 (mptt) cc_final: 0.6789 (mttp) REVERT: j 53 ARG cc_start: 0.8372 (ttm170) cc_final: 0.7021 (ttm170) REVERT: j 61 SER cc_start: 0.8881 (p) cc_final: 0.8569 (p) REVERT: j 63 GLU cc_start: 0.8237 (tt0) cc_final: 0.7859 (tt0) REVERT: j 65 PHE cc_start: 0.8657 (m-80) cc_final: 0.8372 (m-80) REVERT: j 74 ILE cc_start: 0.8912 (mp) cc_final: 0.8585 (mm) REVERT: j 90 LEU cc_start: 0.9094 (mt) cc_final: 0.8783 (mt) REVERT: k 22 ILE cc_start: 0.9367 (pt) cc_final: 0.8837 (pt) REVERT: k 31 ASN cc_start: 0.8739 (t0) cc_final: 0.8450 (t0) REVERT: k 37 THR cc_start: 0.9310 (p) cc_final: 0.8959 (t) REVERT: k 54 PHE cc_start: 0.8062 (m-80) cc_final: 0.7714 (m-80) REVERT: k 88 VAL cc_start: 0.9320 (t) cc_final: 0.8835 (m) REVERT: l 37 ASN cc_start: 0.8017 (m-40) cc_final: 0.7756 (p0) REVERT: l 65 TYR cc_start: 0.8288 (t80) cc_final: 0.8062 (t80) REVERT: l 111 VAL cc_start: 0.8850 (t) cc_final: 0.8640 (p) REVERT: l 128 SER cc_start: 0.8732 (p) cc_final: 0.8506 (p) REVERT: m 29 THR cc_start: 0.9336 (p) cc_final: 0.8984 (p) REVERT: m 31 GLN cc_start: 0.9136 (mt0) cc_final: 0.8519 (mt0) REVERT: m 87 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8434 (ttt90) REVERT: m 109 ARG cc_start: 0.8367 (mtt-85) cc_final: 0.7971 (mtm-85) REVERT: n 6 MET cc_start: 0.8359 (mmm) cc_final: 0.8050 (mmt) REVERT: n 17 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8360 (tptp) REVERT: n 18 VAL cc_start: 0.9306 (m) cc_final: 0.9045 (t) REVERT: n 21 TYR cc_start: 0.8473 (p90) cc_final: 0.7843 (p90) REVERT: n 35 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7630 (ttm-80) REVERT: n 40 CYS cc_start: 0.7617 (t) cc_final: 0.7320 (t) REVERT: n 42 ILE cc_start: 0.9037 (mt) cc_final: 0.8721 (tp) REVERT: n 50 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7667 (tttp) REVERT: o 14 GLU cc_start: 0.8651 (tp30) cc_final: 0.8392 (tm-30) REVERT: o 17 THR cc_start: 0.9037 (p) cc_final: 0.8668 (p) REVERT: o 33 THR cc_start: 0.9081 (p) cc_final: 0.8846 (m) REVERT: o 43 LEU cc_start: 0.9111 (mp) cc_final: 0.8270 (mt) REVERT: o 62 LYS cc_start: 0.8794 (mttt) cc_final: 0.8472 (mmmt) REVERT: o 78 TYR cc_start: 0.8876 (t80) cc_final: 0.8595 (t80) REVERT: o 80 GLU cc_start: 0.8609 (tp30) cc_final: 0.8300 (tp30) REVERT: o 84 LYS cc_start: 0.8943 (mtmm) cc_final: 0.7636 (mtmm) REVERT: p 6 ARG cc_start: 0.8969 (ptt180) cc_final: 0.8739 (ptt90) REVERT: p 8 LYS cc_start: 0.8328 (tttp) cc_final: 0.7514 (tttp) REVERT: p 49 VAL cc_start: 0.7356 (t) cc_final: 0.7021 (t) REVERT: p 71 ARG cc_start: 0.8533 (tpt90) cc_final: 0.8181 (tpt90) REVERT: p 79 ILE cc_start: 0.8700 (mp) cc_final: 0.8495 (mp) REVERT: p 80 MET cc_start: 0.8160 (mmm) cc_final: 0.7883 (mmm) REVERT: q 19 MET cc_start: 0.7757 (mpp) cc_final: 0.7285 (mmp) REVERT: q 32 LYS cc_start: 0.7041 (pptt) cc_final: 0.6800 (mtmm) REVERT: q 40 VAL cc_start: 0.8780 (t) cc_final: 0.8504 (t) REVERT: q 41 LYS cc_start: 0.8688 (pttt) cc_final: 0.8050 (ptpp) REVERT: q 63 ILE cc_start: 0.8712 (pt) cc_final: 0.8335 (pt) REVERT: q 70 SER cc_start: 0.7315 (p) cc_final: 0.7076 (m) REVERT: r 45 LEU cc_start: 0.8954 (mt) cc_final: 0.8462 (mt) REVERT: r 68 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7170 (mmm-85) REVERT: s 26 ASP cc_start: 0.8152 (p0) cc_final: 0.7868 (p0) REVERT: s 66 MET cc_start: 0.8196 (ptp) cc_final: 0.7592 (mtp) REVERT: t 49 THR cc_start: 0.9616 (p) cc_final: 0.9284 (p) REVERT: t 60 LYS cc_start: 0.8921 (mttt) cc_final: 0.7955 (mtpp) REVERT: x 494 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7286 (mmp-170) REVERT: x 595 LEU cc_start: 0.9177 (mt) cc_final: 0.8921 (mt) REVERT: x 658 ASN cc_start: 0.8375 (m-40) cc_final: 0.7862 (m110) REVERT: x 661 ILE cc_start: 0.6240 (mp) cc_final: 0.5987 (tp) REVERT: x 663 ILE cc_start: 0.7819 (mt) cc_final: 0.7365 (mp) REVERT: x 700 THR cc_start: 0.8746 (p) cc_final: 0.8315 (p) REVERT: x 711 ASN cc_start: 0.8076 (p0) cc_final: 0.7740 (p0) outliers start: 7 outliers final: 1 residues processed: 2254 average time/residue: 1.4420 time to fit residues: 5592.3505 Evaluate side-chains 1865 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1863 time to evaluate : 6.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 512 optimal weight: 4.9990 chunk 286 optimal weight: 10.0000 chunk 767 optimal weight: 30.0000 chunk 628 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 924 optimal weight: 5.9990 chunk 998 optimal weight: 20.0000 chunk 823 optimal weight: 6.9990 chunk 916 optimal weight: 20.0000 chunk 315 optimal weight: 6.9990 chunk 741 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 194 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN E 179 ASN E 182 ASN E 189 HIS ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN K 4 GLN L 4 HIS L 38 GLN ** L 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 ASN Q 66 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS U 58 ASN ** W 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 HIS 1 19 HIS 2 4 ASN ** 2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 26 ASN 4 26 HIS 4 38 GLN ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 122 GLN ** c 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 52 GLN ** d 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN ** k 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 35 HIS ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 ASN ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 29 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 68 HIS x 475 HIS ** x 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 159537 Z= 0.361 Angle : 0.805 15.153 238979 Z= 0.403 Chirality : 0.042 0.399 30585 Planarity : 0.006 0.114 12519 Dihedral : 25.432 179.732 80645 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.77 % Favored : 88.05 % Rotamer: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.96 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.10), residues: 5546 helix: -1.48 (0.12), residues: 1639 sheet: -1.45 (0.17), residues: 859 loop : -2.37 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP x 645 HIS 0.015 0.002 HIS x 475 PHE 0.027 0.003 PHE D 119 TYR 0.023 0.003 TYR O 100 ARG 0.010 0.001 ARG W 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2122 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2116 time to evaluate : 6.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 SER cc_start: 0.8737 (p) cc_final: 0.8380 (m) REVERT: C 116 ILE cc_start: 0.9083 (mt) cc_final: 0.8780 (mt) REVERT: C 124 ILE cc_start: 0.9424 (mp) cc_final: 0.9162 (mp) REVERT: C 141 VAL cc_start: 0.8976 (t) cc_final: 0.8455 (p) REVERT: C 259 THR cc_start: 0.8968 (p) cc_final: 0.8250 (t) REVERT: C 273 ARG cc_start: 0.4869 (ptm-80) cc_final: 0.4598 (ptt90) REVERT: D 54 ASP cc_start: 0.6643 (t70) cc_final: 0.6217 (t70) REVERT: D 82 GLU cc_start: 0.6218 (tt0) cc_final: 0.5884 (tt0) REVERT: D 100 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7528 (tm-30) REVERT: D 169 ILE cc_start: 0.8178 (mt) cc_final: 0.7766 (mt) REVERT: D 185 LEU cc_start: 0.9181 (mt) cc_final: 0.8788 (mt) REVERT: D 186 LEU cc_start: 0.9175 (mt) cc_final: 0.8714 (mt) REVERT: E 39 MET cc_start: 0.7441 (tmm) cc_final: 0.7103 (tmm) REVERT: E 40 GLN cc_start: 0.8918 (tt0) cc_final: 0.8447 (tt0) REVERT: E 136 THR cc_start: 0.9210 (p) cc_final: 0.8968 (p) REVERT: E 147 SER cc_start: 0.8551 (p) cc_final: 0.8341 (p) REVERT: E 184 LEU cc_start: 0.9210 (pp) cc_final: 0.8860 (pp) REVERT: E 185 ASP cc_start: 0.8734 (m-30) cc_final: 0.7411 (m-30) REVERT: E 189 HIS cc_start: 0.7752 (m90) cc_final: 0.5835 (m90) REVERT: F 138 PHE cc_start: 0.7406 (p90) cc_final: 0.7034 (p90) REVERT: F 162 THR cc_start: 0.8788 (p) cc_final: 0.8271 (p) REVERT: F 170 LEU cc_start: 0.8767 (mt) cc_final: 0.8491 (mt) REVERT: G 75 ASN cc_start: 0.8910 (m110) cc_final: 0.8640 (m110) REVERT: J 16 TRP cc_start: 0.8872 (m100) cc_final: 0.8523 (m100) REVERT: J 56 ILE cc_start: 0.9218 (mt) cc_final: 0.8949 (mt) REVERT: J 119 MET cc_start: 0.8042 (mtm) cc_final: 0.7839 (mtp) REVERT: K 2 ILE cc_start: 0.8308 (mt) cc_final: 0.7847 (mm) REVERT: K 5 GLU cc_start: 0.8696 (mp0) cc_final: 0.8120 (mp0) REVERT: K 25 LEU cc_start: 0.7564 (mm) cc_final: 0.7344 (mm) REVERT: K 54 LYS cc_start: 0.7901 (tttp) cc_final: 0.7315 (ttpt) REVERT: K 64 ARG cc_start: 0.6962 (ptt-90) cc_final: 0.6687 (ptt90) REVERT: L 23 ILE cc_start: 0.7489 (pt) cc_final: 0.7098 (tp) REVERT: L 29 LYS cc_start: 0.7630 (tmmt) cc_final: 0.6737 (tptt) REVERT: M 25 THR cc_start: 0.8886 (p) cc_final: 0.8667 (p) REVERT: M 29 PHE cc_start: 0.7550 (m-10) cc_final: 0.7122 (m-10) REVERT: M 41 TRP cc_start: 0.8788 (m-10) cc_final: 0.8465 (m-10) REVERT: M 44 ASN cc_start: 0.8610 (p0) cc_final: 0.8355 (p0) REVERT: M 123 HIS cc_start: 0.8179 (m-70) cc_final: 0.7857 (m-70) REVERT: M 124 LYS cc_start: 0.9110 (mmtm) cc_final: 0.8826 (mmmt) REVERT: M 128 LYS cc_start: 0.8921 (tttt) cc_final: 0.8537 (tttp) REVERT: N 20 LEU cc_start: 0.9022 (mt) cc_final: 0.8753 (mt) REVERT: N 38 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8606 (mtpp) REVERT: N 49 THR cc_start: 0.8940 (p) cc_final: 0.8737 (p) REVERT: N 81 GLN cc_start: 0.8796 (mt0) cc_final: 0.8256 (mt0) REVERT: N 82 LYS cc_start: 0.8905 (tttm) cc_final: 0.8195 (tttt) REVERT: N 95 GLN cc_start: 0.8483 (mt0) cc_final: 0.8142 (mp10) REVERT: O 17 ARG cc_start: 0.8515 (ttm110) cc_final: 0.7954 (mtp180) REVERT: O 27 GLU cc_start: 0.9306 (pm20) cc_final: 0.9035 (pm20) REVERT: O 38 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8682 (mmmm) REVERT: O 75 THR cc_start: 0.9500 (m) cc_final: 0.9188 (p) REVERT: O 79 GLU cc_start: 0.8540 (mp0) cc_final: 0.8092 (mp0) REVERT: O 90 ILE cc_start: 0.8790 (tp) cc_final: 0.8451 (tp) REVERT: O 92 ASP cc_start: 0.8024 (m-30) cc_final: 0.7432 (m-30) REVERT: O 118 LEU cc_start: 0.9053 (mm) cc_final: 0.8677 (mm) REVERT: P 5 ILE cc_start: 0.8369 (mm) cc_final: 0.8042 (mt) REVERT: P 88 ARG cc_start: 0.8379 (mtp-110) cc_final: 0.7561 (mtp-110) REVERT: Q 16 LYS cc_start: 0.8615 (tppt) cc_final: 0.8351 (tppt) REVERT: Q 37 GLN cc_start: 0.7772 (mt0) cc_final: 0.6448 (tt0) REVERT: Q 45 TYR cc_start: 0.8711 (m-10) cc_final: 0.7992 (m-10) REVERT: Q 56 ASP cc_start: 0.7499 (t70) cc_final: 0.7268 (t70) REVERT: Q 80 MET cc_start: 0.8515 (mmm) cc_final: 0.8294 (tpp) REVERT: R 16 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7454 (tm-30) REVERT: R 35 PHE cc_start: 0.8448 (m-80) cc_final: 0.8018 (m-10) REVERT: R 69 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8328 (tppt) REVERT: S 23 LEU cc_start: 0.7870 (mp) cc_final: 0.7647 (mp) REVERT: S 31 GLU cc_start: 0.8458 (tt0) cc_final: 0.8097 (tp30) REVERT: S 37 ASN cc_start: 0.8228 (m110) cc_final: 0.7878 (m110) REVERT: S 62 TYR cc_start: 0.7825 (m-80) cc_final: 0.7427 (m-80) REVERT: S 68 ASN cc_start: 0.7776 (p0) cc_final: 0.6665 (p0) REVERT: S 70 VAL cc_start: 0.8709 (t) cc_final: 0.8381 (p) REVERT: S 84 ARG cc_start: 0.6490 (mmt-90) cc_final: 0.5509 (tpt170) REVERT: S 96 ILE cc_start: 0.7992 (mm) cc_final: 0.7727 (tt) REVERT: T 13 ILE cc_start: 0.9178 (mp) cc_final: 0.8675 (tp) REVERT: T 21 MET cc_start: 0.8799 (mtm) cc_final: 0.8233 (mtt) REVERT: T 28 PHE cc_start: 0.8194 (m-80) cc_final: 0.7614 (m-80) REVERT: T 38 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8556 (mm-30) REVERT: T 57 MET cc_start: 0.7423 (mtp) cc_final: 0.6891 (mtp) REVERT: U 7 ASP cc_start: 0.8093 (m-30) cc_final: 0.7889 (m-30) REVERT: U 16 ASP cc_start: 0.7986 (t0) cc_final: 0.7725 (t0) REVERT: U 56 ILE cc_start: 0.8573 (mm) cc_final: 0.8172 (tp) REVERT: U 64 HIS cc_start: 0.8620 (t-90) cc_final: 0.8015 (t70) REVERT: U 86 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6783 (tm-30) REVERT: U 99 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8443 (mm-40) REVERT: V 20 ASN cc_start: 0.8905 (m-40) cc_final: 0.8380 (m-40) REVERT: X 53 MET cc_start: 0.8899 (ptp) cc_final: 0.8513 (ptm) REVERT: X 56 VAL cc_start: 0.9405 (t) cc_final: 0.8992 (t) REVERT: 1 27 MET cc_start: 0.7509 (mmm) cc_final: 0.7084 (mmm) REVERT: 2 16 ASN cc_start: 0.9005 (m-40) cc_final: 0.8725 (m-40) REVERT: 2 25 ASN cc_start: 0.8795 (m-40) cc_final: 0.8376 (m-40) REVERT: 2 29 ARG cc_start: 0.8436 (ttm170) cc_final: 0.8060 (mtt-85) REVERT: 2 47 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7134 (tm-30) REVERT: 3 1 MET cc_start: 0.5029 (mmm) cc_final: 0.4769 (mmm) REVERT: 3 14 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7770 (ttmm) REVERT: 4 21 LYS cc_start: 0.5626 (mmmt) cc_final: 0.5327 (mmtt) REVERT: 4 23 LYS cc_start: 0.7381 (tmmt) cc_final: 0.7069 (pttp) REVERT: 4 39 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8858 (ttmm) REVERT: 4 56 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8299 (ttmm) REVERT: 4 62 LEU cc_start: 0.8398 (pp) cc_final: 0.8138 (pp) REVERT: 5 1 MET cc_start: 0.9028 (tpp) cc_final: 0.8693 (tpp) REVERT: 5 4 ARG cc_start: 0.8219 (ptp-170) cc_final: 0.7968 (ptm160) REVERT: 5 19 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7708 (ptm160) REVERT: 5 34 GLN cc_start: 0.8386 (mt0) cc_final: 0.8000 (tt0) REVERT: Z 13 THR cc_start: 0.8284 (p) cc_final: 0.8066 (t) REVERT: b 26 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8653 (mmtp) REVERT: b 45 LYS cc_start: 0.9448 (mtmt) cc_final: 0.9216 (mtmt) REVERT: b 104 PHE cc_start: 0.7426 (t80) cc_final: 0.7057 (t80) REVERT: b 108 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8755 (mm110) REVERT: b 171 ILE cc_start: 0.8153 (mp) cc_final: 0.7879 (mp) REVERT: b 178 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7914 (tptp) REVERT: c 31 PHE cc_start: 0.8834 (m-80) cc_final: 0.8443 (m-80) REVERT: c 33 HIS cc_start: 0.8543 (m90) cc_final: 0.7815 (m90) REVERT: c 66 THR cc_start: 0.8456 (t) cc_final: 0.6822 (t) REVERT: c 200 TRP cc_start: 0.7575 (p90) cc_final: 0.7341 (p90) REVERT: d 47 TYR cc_start: 0.8169 (t80) cc_final: 0.7823 (t80) REVERT: d 50 GLN cc_start: 0.9272 (mt0) cc_final: 0.8470 (mm-40) REVERT: d 59 HIS cc_start: 0.8614 (m-70) cc_final: 0.7831 (m-70) REVERT: d 120 LEU cc_start: 0.8490 (mp) cc_final: 0.8208 (mp) REVERT: d 198 TYR cc_start: 0.8091 (m-80) cc_final: 0.7628 (m-10) REVERT: e 65 GLU cc_start: 0.7319 (tt0) cc_final: 0.7098 (tt0) REVERT: e 88 ARG cc_start: 0.7374 (mtt-85) cc_final: 0.7115 (mmt180) REVERT: e 141 LEU cc_start: 0.9229 (mt) cc_final: 0.8860 (tt) REVERT: e 147 LEU cc_start: 0.9094 (mt) cc_final: 0.8452 (mt) REVERT: f 60 TYR cc_start: 0.8193 (m-80) cc_final: 0.7610 (m-80) REVERT: f 89 ILE cc_start: 0.8496 (mp) cc_final: 0.8287 (mp) REVERT: g 17 ILE cc_start: 0.8698 (pt) cc_final: 0.8404 (pt) REVERT: g 28 ASN cc_start: 0.8847 (m-40) cc_final: 0.8474 (m-40) REVERT: g 31 MET cc_start: 0.9037 (ttm) cc_final: 0.8202 (ttt) REVERT: g 45 LYS cc_start: 0.9329 (tppt) cc_final: 0.8953 (tppt) REVERT: g 49 ILE cc_start: 0.9125 (mt) cc_final: 0.8919 (mt) REVERT: g 61 VAL cc_start: 0.9156 (t) cc_final: 0.8794 (t) REVERT: g 68 ASN cc_start: 0.9336 (m-40) cc_final: 0.8556 (t0) REVERT: g 85 TYR cc_start: 0.6541 (m-10) cc_final: 0.6253 (m-80) REVERT: g 115 THR cc_start: 0.8756 (p) cc_final: 0.7632 (p) REVERT: g 122 ASN cc_start: 0.8929 (m-40) cc_final: 0.8486 (m-40) REVERT: g 130 ASN cc_start: 0.8450 (p0) cc_final: 0.8192 (p0) REVERT: g 135 VAL cc_start: 0.9292 (m) cc_final: 0.8449 (m) REVERT: h 46 ILE cc_start: 0.9077 (mm) cc_final: 0.8833 (mm) REVERT: h 66 TYR cc_start: 0.8158 (m-10) cc_final: 0.7630 (m-80) REVERT: h 98 LEU cc_start: 0.9169 (mt) cc_final: 0.8670 (mm) REVERT: h 101 LEU cc_start: 0.9195 (tt) cc_final: 0.8991 (tt) REVERT: h 112 VAL cc_start: 0.9168 (t) cc_final: 0.8807 (m) REVERT: h 126 GLU cc_start: 0.8554 (tp30) cc_final: 0.8328 (tp30) REVERT: h 127 VAL cc_start: 0.9185 (t) cc_final: 0.8891 (t) REVERT: i 46 GLU cc_start: 0.8419 (pt0) cc_final: 0.7950 (pt0) REVERT: i 81 HIS cc_start: 0.8212 (t70) cc_final: 0.7473 (t-90) REVERT: j 10 LEU cc_start: 0.8978 (mm) cc_final: 0.8748 (mm) REVERT: j 27 GLU cc_start: 0.8505 (pp20) cc_final: 0.8300 (pp20) REVERT: j 61 SER cc_start: 0.8895 (p) cc_final: 0.8539 (p) REVERT: j 63 GLU cc_start: 0.8267 (tt0) cc_final: 0.7965 (tt0) REVERT: j 67 MET cc_start: 0.8280 (tmm) cc_final: 0.7940 (ttm) REVERT: j 90 LEU cc_start: 0.9140 (mt) cc_final: 0.8744 (mt) REVERT: k 22 ILE cc_start: 0.9353 (pt) cc_final: 0.8970 (pt) REVERT: k 24 HIS cc_start: 0.7460 (m170) cc_final: 0.7246 (m170) REVERT: k 37 THR cc_start: 0.9128 (p) cc_final: 0.8926 (t) REVERT: k 54 PHE cc_start: 0.7887 (m-80) cc_final: 0.7670 (m-80) REVERT: k 83 THR cc_start: 0.9198 (p) cc_final: 0.8835 (p) REVERT: k 88 VAL cc_start: 0.9376 (t) cc_final: 0.8896 (m) REVERT: l 34 GLU cc_start: 0.8529 (pp20) cc_final: 0.8024 (pp20) REVERT: l 35 HIS cc_start: 0.6969 (m-70) cc_final: 0.6338 (m170) REVERT: l 49 ARG cc_start: 0.7626 (ttp-170) cc_final: 0.7046 (ttp-170) REVERT: l 65 TYR cc_start: 0.8452 (t80) cc_final: 0.8196 (t80) REVERT: m 29 THR cc_start: 0.9477 (p) cc_final: 0.9229 (p) REVERT: m 31 GLN cc_start: 0.9112 (mt0) cc_final: 0.8739 (mt0) REVERT: m 53 LEU cc_start: 0.8432 (mt) cc_final: 0.8165 (mt) REVERT: m 81 ILE cc_start: 0.8834 (tt) cc_final: 0.8380 (tp) REVERT: m 87 ARG cc_start: 0.8951 (ttp80) cc_final: 0.8551 (ttt90) REVERT: m 100 GLN cc_start: 0.8932 (mp10) cc_final: 0.8678 (mp10) REVERT: m 109 ARG cc_start: 0.8703 (mtt-85) cc_final: 0.8342 (mtm-85) REVERT: n 4 LYS cc_start: 0.9000 (mttt) cc_final: 0.8573 (mttt) REVERT: n 6 MET cc_start: 0.8616 (mmm) cc_final: 0.8414 (mmt) REVERT: n 9 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8312 (tttt) REVERT: n 17 LYS cc_start: 0.9110 (mmmt) cc_final: 0.8364 (tptp) REVERT: n 19 GLN cc_start: 0.8707 (mt0) cc_final: 0.8216 (mt0) REVERT: n 42 ILE cc_start: 0.9202 (mt) cc_final: 0.8928 (tp) REVERT: n 46 GLU cc_start: 0.7827 (tt0) cc_final: 0.7623 (tt0) REVERT: n 50 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7812 (tttp) REVERT: n 57 LYS cc_start: 0.8478 (pttt) cc_final: 0.8172 (pttt) REVERT: o 17 THR cc_start: 0.9123 (p) cc_final: 0.8581 (p) REVERT: o 43 LEU cc_start: 0.9239 (mp) cc_final: 0.8873 (mp) REVERT: o 62 LYS cc_start: 0.8830 (mttt) cc_final: 0.8587 (mmmt) REVERT: o 80 GLU cc_start: 0.8583 (tp30) cc_final: 0.8287 (tp30) REVERT: o 84 LYS cc_start: 0.8791 (mtmm) cc_final: 0.7658 (mtmm) REVERT: p 6 ARG cc_start: 0.9098 (ptt180) cc_final: 0.8658 (ptt90) REVERT: p 65 LYS cc_start: 0.8868 (mttt) cc_final: 0.8598 (mttm) REVERT: p 71 ARG cc_start: 0.8593 (tmt-80) cc_final: 0.7968 (tpt90) REVERT: p 79 ILE cc_start: 0.8832 (mp) cc_final: 0.8606 (mp) REVERT: p 80 MET cc_start: 0.8235 (mmm) cc_final: 0.7887 (mmm) REVERT: q 19 MET cc_start: 0.7688 (mpp) cc_final: 0.7297 (mmp) REVERT: q 41 LYS cc_start: 0.8715 (pttt) cc_final: 0.8309 (ptpt) REVERT: q 70 SER cc_start: 0.7659 (p) cc_final: 0.7448 (m) REVERT: r 33 LEU cc_start: 0.9313 (mt) cc_final: 0.8692 (tp) REVERT: r 36 LYS cc_start: 0.9286 (mtmm) cc_final: 0.8862 (mttp) REVERT: r 45 LEU cc_start: 0.9014 (mt) cc_final: 0.8541 (mt) REVERT: r 48 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.7383 (mtt180) REVERT: s 26 ASP cc_start: 0.8248 (p0) cc_final: 0.7894 (p0) REVERT: s 43 GLN cc_start: 0.9483 (pm20) cc_final: 0.9249 (pm20) REVERT: t 10 ARG cc_start: 0.8833 (mmm160) cc_final: 0.8625 (tpp-160) REVERT: t 60 LYS cc_start: 0.8904 (mttt) cc_final: 0.8318 (tppt) REVERT: t 63 LYS cc_start: 0.7674 (mtpp) cc_final: 0.7431 (mtpp) REVERT: t 70 ASN cc_start: 0.8824 (m-40) cc_final: 0.8413 (p0) REVERT: x 395 TYR cc_start: 0.7430 (m-80) cc_final: 0.7229 (m-10) REVERT: x 595 LEU cc_start: 0.9288 (mt) cc_final: 0.9045 (mt) REVERT: x 658 ASN cc_start: 0.8454 (m-40) cc_final: 0.7973 (m-40) REVERT: x 700 THR cc_start: 0.8920 (p) cc_final: 0.8465 (p) REVERT: x 731 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7393 (ttp80) outliers start: 6 outliers final: 3 residues processed: 2120 average time/residue: 1.3272 time to fit residues: 4804.0205 Evaluate side-chains 1759 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1756 time to evaluate : 6.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 913 optimal weight: 5.9990 chunk 694 optimal weight: 10.0000 chunk 479 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 441 optimal weight: 9.9990 chunk 620 optimal weight: 10.0000 chunk 927 optimal weight: 7.9990 chunk 982 optimal weight: 5.9990 chunk 484 optimal weight: 2.9990 chunk 879 optimal weight: 0.8980 chunk 264 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 62 ASN E 9 GLN E 75 GLN E 179 ASN E 182 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN G 23 ASN J 96 ASN K 4 GLN ** L 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS P 2 GLN ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** W 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 HIS 2 4 ASN ** 2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 122 GLN c 136 GLN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 ASN ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 121 ASN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 59 ASN m 32 GLN o 28 GLN ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 HIS t 68 HIS t 70 ASN ** x 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 604 ASN ** x 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 159537 Z= 0.223 Angle : 0.670 14.899 238979 Z= 0.342 Chirality : 0.038 0.385 30585 Planarity : 0.005 0.105 12519 Dihedral : 25.209 179.925 80645 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.10 % Favored : 89.79 % Rotamer: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.96 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.11), residues: 5546 helix: -1.17 (0.12), residues: 1651 sheet: -1.36 (0.17), residues: 880 loop : -2.34 (0.11), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP x 645 HIS 0.012 0.001 HIS t 68 PHE 0.020 0.002 PHE V 80 TYR 0.029 0.002 TYR b 90 ARG 0.010 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2115 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2110 time to evaluate : 6.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.7410 (mt0) cc_final: 0.7095 (mt0) REVERT: C 115 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 116 ILE cc_start: 0.8979 (mt) cc_final: 0.8734 (mt) REVERT: C 124 ILE cc_start: 0.9438 (mp) cc_final: 0.9068 (mp) REVERT: D 54 ASP cc_start: 0.6630 (t70) cc_final: 0.6426 (t70) REVERT: D 82 GLU cc_start: 0.6210 (tt0) cc_final: 0.5711 (tt0) REVERT: D 100 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7537 (tm-30) REVERT: D 146 MET cc_start: 0.7647 (mmm) cc_final: 0.7085 (mmm) REVERT: D 169 ILE cc_start: 0.8113 (mt) cc_final: 0.7833 (mt) REVERT: D 185 LEU cc_start: 0.9152 (mt) cc_final: 0.8658 (mp) REVERT: D 186 LEU cc_start: 0.9067 (mt) cc_final: 0.8650 (mt) REVERT: E 39 MET cc_start: 0.7200 (tmm) cc_final: 0.6926 (tmm) REVERT: E 185 ASP cc_start: 0.8632 (m-30) cc_final: 0.7878 (m-30) REVERT: E 189 HIS cc_start: 0.7393 (m90) cc_final: 0.6029 (m90) REVERT: F 59 PHE cc_start: 0.8578 (m-80) cc_final: 0.8359 (m-80) REVERT: F 78 ARG cc_start: 0.7638 (ttm110) cc_final: 0.7415 (ttp-110) REVERT: F 138 PHE cc_start: 0.7105 (p90) cc_final: 0.6813 (p90) REVERT: F 154 ILE cc_start: 0.8183 (mm) cc_final: 0.7717 (mm) REVERT: F 158 THR cc_start: 0.8825 (p) cc_final: 0.8594 (p) REVERT: G 75 ASN cc_start: 0.8723 (m110) cc_final: 0.8309 (t0) REVERT: G 102 ASN cc_start: 0.8894 (t0) cc_final: 0.8683 (t0) REVERT: G 107 ASN cc_start: 0.8448 (m-40) cc_final: 0.8234 (m-40) REVERT: G 172 ARG cc_start: 0.8535 (mmp80) cc_final: 0.8110 (mmm160) REVERT: J 50 ASP cc_start: 0.8228 (t0) cc_final: 0.5794 (t70) REVERT: J 75 TYR cc_start: 0.7899 (m-10) cc_final: 0.7281 (m-10) REVERT: J 96 ASN cc_start: 0.6460 (m-40) cc_final: 0.6247 (m110) REVERT: J 119 MET cc_start: 0.8267 (mtm) cc_final: 0.7521 (mmm) REVERT: K 1 MET cc_start: 0.6669 (mmt) cc_final: 0.6162 (mmt) REVERT: K 2 ILE cc_start: 0.8508 (mt) cc_final: 0.8133 (mm) REVERT: K 5 GLU cc_start: 0.8624 (mp0) cc_final: 0.7996 (mp0) REVERT: K 54 LYS cc_start: 0.7884 (tttp) cc_final: 0.7336 (ttpt) REVERT: K 94 ARG cc_start: 0.7045 (ptm160) cc_final: 0.6746 (ptm160) REVERT: L 23 ILE cc_start: 0.7415 (pt) cc_final: 0.7034 (tp) REVERT: M 2 LEU cc_start: 0.9270 (mp) cc_final: 0.9054 (mp) REVERT: M 3 LEU cc_start: 0.9043 (mm) cc_final: 0.8170 (mm) REVERT: M 25 THR cc_start: 0.8853 (p) cc_final: 0.8637 (p) REVERT: M 41 TRP cc_start: 0.8619 (m-10) cc_final: 0.8411 (m-10) REVERT: M 124 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8832 (mmmt) REVERT: M 128 LYS cc_start: 0.8892 (tttt) cc_final: 0.8322 (tttt) REVERT: N 49 THR cc_start: 0.8780 (p) cc_final: 0.8568 (p) REVERT: N 81 GLN cc_start: 0.8597 (mt0) cc_final: 0.8234 (mt0) REVERT: N 82 LYS cc_start: 0.8837 (tttm) cc_final: 0.8102 (tttt) REVERT: N 95 GLN cc_start: 0.8154 (mt0) cc_final: 0.7785 (mp10) REVERT: O 15 HIS cc_start: 0.8325 (t70) cc_final: 0.7982 (t70) REVERT: O 39 HIS cc_start: 0.7242 (m-70) cc_final: 0.6822 (m90) REVERT: O 43 GLN cc_start: 0.5715 (tp40) cc_final: 0.5378 (tp40) REVERT: O 44 ILE cc_start: 0.8171 (mp) cc_final: 0.7686 (mp) REVERT: O 45 ILE cc_start: 0.8677 (mm) cc_final: 0.8296 (mm) REVERT: O 79 GLU cc_start: 0.8377 (mp0) cc_final: 0.8015 (mp0) REVERT: O 90 ILE cc_start: 0.8713 (tp) cc_final: 0.8202 (tp) REVERT: O 92 ASP cc_start: 0.7911 (m-30) cc_final: 0.7068 (m-30) REVERT: P 5 ILE cc_start: 0.8384 (mm) cc_final: 0.8023 (mt) REVERT: Q 16 LYS cc_start: 0.8622 (tppt) cc_final: 0.8404 (tppt) REVERT: Q 37 GLN cc_start: 0.7200 (mt0) cc_final: 0.6118 (tt0) REVERT: Q 45 TYR cc_start: 0.8506 (m-10) cc_final: 0.7934 (m-10) REVERT: R 35 PHE cc_start: 0.8520 (m-80) cc_final: 0.8302 (m-10) REVERT: R 69 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8288 (tppt) REVERT: S 31 GLU cc_start: 0.8350 (tt0) cc_final: 0.8117 (mm-30) REVERT: S 62 TYR cc_start: 0.7407 (m-80) cc_final: 0.6915 (m-80) REVERT: S 65 ASP cc_start: 0.8664 (t0) cc_final: 0.8091 (t70) REVERT: S 68 ASN cc_start: 0.7585 (p0) cc_final: 0.7256 (p0) REVERT: S 70 VAL cc_start: 0.8603 (t) cc_final: 0.8351 (p) REVERT: S 84 ARG cc_start: 0.6276 (mmt-90) cc_final: 0.5224 (tpt170) REVERT: S 96 ILE cc_start: 0.7871 (mm) cc_final: 0.7652 (tt) REVERT: S 106 VAL cc_start: 0.8450 (t) cc_final: 0.7650 (t) REVERT: T 13 ILE cc_start: 0.9098 (mp) cc_final: 0.8672 (tp) REVERT: T 21 MET cc_start: 0.8828 (mtm) cc_final: 0.8253 (mtt) REVERT: T 28 PHE cc_start: 0.7977 (m-80) cc_final: 0.7620 (m-80) REVERT: T 37 THR cc_start: 0.8662 (p) cc_final: 0.8435 (p) REVERT: T 57 MET cc_start: 0.7430 (mtp) cc_final: 0.6851 (mtp) REVERT: T 65 ARG cc_start: 0.7115 (tmm160) cc_final: 0.6556 (tmt170) REVERT: U 56 ILE cc_start: 0.8456 (mm) cc_final: 0.8219 (tp) REVERT: U 64 HIS cc_start: 0.8466 (t-90) cc_final: 0.7914 (t70) REVERT: U 86 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6742 (tm-30) REVERT: U 99 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8346 (mm-40) REVERT: V 22 ARG cc_start: 0.7221 (pmt170) cc_final: 0.6821 (ptt-90) REVERT: X 24 GLU cc_start: 0.8593 (pt0) cc_final: 0.8224 (pt0) REVERT: X 28 LEU cc_start: 0.9027 (mm) cc_final: 0.8774 (tp) REVERT: X 43 ILE cc_start: 0.9271 (mp) cc_final: 0.8999 (mp) REVERT: Y 29 LYS cc_start: 0.8475 (mppt) cc_final: 0.7842 (mppt) REVERT: Y 30 LYS cc_start: 0.8768 (mttt) cc_final: 0.8391 (mmmt) REVERT: Y 32 ASN cc_start: 0.8240 (m-40) cc_final: 0.8025 (m-40) REVERT: 1 21 LYS cc_start: 0.7362 (pttt) cc_final: 0.6418 (mmtm) REVERT: 1 27 MET cc_start: 0.7409 (mmm) cc_final: 0.7155 (mmm) REVERT: 2 29 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8040 (mtt-85) REVERT: 2 47 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7129 (tm-30) REVERT: 3 1 MET cc_start: 0.4937 (mmm) cc_final: 0.4471 (mmp) REVERT: 4 4 MET cc_start: 0.8612 (ttm) cc_final: 0.8079 (mmm) REVERT: 4 21 LYS cc_start: 0.5567 (mmmt) cc_final: 0.5357 (mmtt) REVERT: 4 56 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8121 (ttmm) REVERT: 5 1 MET cc_start: 0.8888 (tpp) cc_final: 0.8600 (tpp) REVERT: 5 4 ARG cc_start: 0.8135 (ptp-170) cc_final: 0.7816 (ptm160) REVERT: 5 34 GLN cc_start: 0.8299 (mt0) cc_final: 0.7864 (tt0) REVERT: Z 10 LYS cc_start: 0.7573 (pttm) cc_final: 0.7096 (mtmm) REVERT: Z 28 LYS cc_start: 0.7353 (tmmt) cc_final: 0.7143 (ttpt) REVERT: b 45 LYS cc_start: 0.9478 (mtmt) cc_final: 0.9182 (mtmt) REVERT: b 104 PHE cc_start: 0.7557 (t80) cc_final: 0.7041 (t80) REVERT: b 178 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7904 (tptp) REVERT: b 184 ILE cc_start: 0.8825 (pt) cc_final: 0.8568 (pt) REVERT: c 31 PHE cc_start: 0.8650 (m-80) cc_final: 0.8157 (m-80) REVERT: d 47 TYR cc_start: 0.8235 (t80) cc_final: 0.7794 (t80) REVERT: d 50 GLN cc_start: 0.9327 (mt0) cc_final: 0.8607 (mm-40) REVERT: d 59 HIS cc_start: 0.8148 (m-70) cc_final: 0.7551 (m-70) REVERT: d 120 LEU cc_start: 0.8414 (mp) cc_final: 0.8080 (mp) REVERT: d 198 TYR cc_start: 0.8109 (m-80) cc_final: 0.7554 (m-10) REVERT: e 88 ARG cc_start: 0.7469 (mtt-85) cc_final: 0.7164 (mmt180) REVERT: e 95 LEU cc_start: 0.8355 (pt) cc_final: 0.7965 (pt) REVERT: e 141 LEU cc_start: 0.9141 (mt) cc_final: 0.8798 (tt) REVERT: e 147 LEU cc_start: 0.9037 (mt) cc_final: 0.8527 (mt) REVERT: e 152 ASP cc_start: 0.9060 (m-30) cc_final: 0.8801 (m-30) REVERT: f 5 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7206 (tm-30) REVERT: f 10 ILE cc_start: 0.8618 (mp) cc_final: 0.8298 (mp) REVERT: f 46 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7960 (ttm110) REVERT: f 89 ILE cc_start: 0.8644 (mp) cc_final: 0.8439 (mp) REVERT: g 11 ASP cc_start: 0.7790 (p0) cc_final: 0.7287 (p0) REVERT: g 17 ILE cc_start: 0.8807 (pt) cc_final: 0.8093 (pt) REVERT: g 31 MET cc_start: 0.9057 (ttm) cc_final: 0.8270 (ttt) REVERT: g 68 ASN cc_start: 0.9318 (m-40) cc_final: 0.8507 (t0) REVERT: g 122 ASN cc_start: 0.8886 (m-40) cc_final: 0.8399 (m-40) REVERT: g 130 ASN cc_start: 0.8403 (p0) cc_final: 0.8118 (p0) REVERT: g 135 VAL cc_start: 0.9047 (m) cc_final: 0.8420 (m) REVERT: h 39 ILE cc_start: 0.8614 (mm) cc_final: 0.8023 (mm) REVERT: h 41 LYS cc_start: 0.9169 (tptm) cc_final: 0.8718 (mmmm) REVERT: h 66 TYR cc_start: 0.8111 (m-10) cc_final: 0.7800 (m-80) REVERT: h 98 LEU cc_start: 0.9133 (mt) cc_final: 0.8679 (mm) REVERT: h 101 LEU cc_start: 0.9091 (tt) cc_final: 0.8757 (tt) REVERT: h 112 VAL cc_start: 0.9203 (t) cc_final: 0.8874 (m) REVERT: h 127 VAL cc_start: 0.9197 (t) cc_final: 0.8891 (t) REVERT: i 25 GLU cc_start: 0.6833 (pp20) cc_final: 0.6570 (pp20) REVERT: i 49 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8860 (mtmm) REVERT: i 81 HIS cc_start: 0.8258 (t70) cc_final: 0.7838 (t-90) REVERT: j 20 GLN cc_start: 0.8935 (mm110) cc_final: 0.8717 (mm-40) REVERT: j 61 SER cc_start: 0.9051 (p) cc_final: 0.8709 (p) REVERT: j 90 LEU cc_start: 0.9134 (mt) cc_final: 0.8834 (mt) REVERT: j 92 LEU cc_start: 0.8927 (mm) cc_final: 0.8243 (mm) REVERT: k 36 ILE cc_start: 0.9193 (pt) cc_final: 0.8930 (pt) REVERT: k 54 PHE cc_start: 0.7865 (m-80) cc_final: 0.7246 (m-80) REVERT: k 79 HIS cc_start: 0.7179 (m-70) cc_final: 0.6534 (m-70) REVERT: k 83 THR cc_start: 0.9145 (p) cc_final: 0.8883 (p) REVERT: k 88 VAL cc_start: 0.9375 (t) cc_final: 0.8967 (m) REVERT: l 35 HIS cc_start: 0.7574 (m-70) cc_final: 0.7011 (m90) REVERT: l 49 ARG cc_start: 0.7585 (ttp-170) cc_final: 0.7043 (ttp-170) REVERT: l 65 TYR cc_start: 0.8400 (t80) cc_final: 0.8198 (t80) REVERT: l 128 SER cc_start: 0.8772 (p) cc_final: 0.8531 (p) REVERT: m 55 LYS cc_start: 0.9480 (tttt) cc_final: 0.9177 (ptmt) REVERT: m 81 ILE cc_start: 0.8707 (tt) cc_final: 0.8360 (tp) REVERT: m 87 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8390 (ttt90) REVERT: m 100 GLN cc_start: 0.8922 (mp10) cc_final: 0.8607 (mp10) REVERT: m 109 ARG cc_start: 0.8633 (mtt-85) cc_final: 0.8330 (mtt90) REVERT: n 6 MET cc_start: 0.8396 (mmm) cc_final: 0.8163 (mmt) REVERT: n 7 ILE cc_start: 0.9301 (mt) cc_final: 0.8656 (mt) REVERT: n 9 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8261 (tttt) REVERT: n 17 LYS cc_start: 0.9121 (mmmt) cc_final: 0.8445 (tptp) REVERT: n 21 TYR cc_start: 0.8580 (p90) cc_final: 0.8129 (p90) REVERT: n 35 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7307 (ttm-80) REVERT: n 42 ILE cc_start: 0.9229 (mt) cc_final: 0.8926 (tp) REVERT: o 7 ARG cc_start: 0.8645 (tpt90) cc_final: 0.8243 (tpt90) REVERT: o 11 LEU cc_start: 0.9240 (mt) cc_final: 0.8772 (mt) REVERT: o 33 THR cc_start: 0.9420 (m) cc_final: 0.9163 (m) REVERT: o 43 LEU cc_start: 0.9289 (mp) cc_final: 0.9055 (tp) REVERT: o 54 ARG cc_start: 0.8496 (ttt90) cc_final: 0.8064 (ttt90) REVERT: o 62 LYS cc_start: 0.8863 (mttt) cc_final: 0.8621 (mmmt) REVERT: o 78 TYR cc_start: 0.8772 (t80) cc_final: 0.8498 (t80) REVERT: p 6 ARG cc_start: 0.9060 (ptt180) cc_final: 0.8770 (ptp90) REVERT: p 49 VAL cc_start: 0.6572 (t) cc_final: 0.6335 (t) REVERT: p 65 LYS cc_start: 0.8770 (mttt) cc_final: 0.8483 (mttm) REVERT: p 79 ILE cc_start: 0.8883 (mp) cc_final: 0.8612 (mp) REVERT: p 83 PHE cc_start: 0.8828 (t80) cc_final: 0.8346 (t80) REVERT: p 87 LYS cc_start: 0.8862 (pttp) cc_final: 0.8648 (pttm) REVERT: q 19 MET cc_start: 0.7460 (mpp) cc_final: 0.7121 (mmp) REVERT: q 27 VAL cc_start: 0.8631 (t) cc_final: 0.8145 (m) REVERT: q 41 LYS cc_start: 0.8682 (pttt) cc_final: 0.8077 (ptpp) REVERT: r 33 LEU cc_start: 0.9327 (mt) cc_final: 0.8657 (tp) REVERT: r 36 LYS cc_start: 0.9243 (mtmm) cc_final: 0.8966 (mttp) REVERT: r 43 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7937 (mttp) REVERT: r 45 LEU cc_start: 0.8924 (mt) cc_final: 0.8424 (mt) REVERT: r 48 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7438 (mtt180) REVERT: r 52 THR cc_start: 0.9473 (p) cc_final: 0.9234 (p) REVERT: r 75 TYR cc_start: 0.8306 (m-80) cc_final: 0.7554 (m-80) REVERT: s 22 LEU cc_start: 0.8916 (tp) cc_final: 0.8544 (tp) REVERT: s 43 GLN cc_start: 0.9499 (pm20) cc_final: 0.9263 (pm20) REVERT: t 10 ARG cc_start: 0.8766 (mmm160) cc_final: 0.8539 (tpp-160) REVERT: t 58 ILE cc_start: 0.9113 (tt) cc_final: 0.8903 (tt) REVERT: t 63 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7518 (mtpt) REVERT: t 70 ASN cc_start: 0.8836 (m110) cc_final: 0.8355 (t0) REVERT: t 71 THR cc_start: 0.8696 (m) cc_final: 0.8232 (m) REVERT: x 595 LEU cc_start: 0.9316 (mt) cc_final: 0.9001 (mt) REVERT: x 658 ASN cc_start: 0.8533 (m-40) cc_final: 0.8043 (m110) REVERT: x 661 ILE cc_start: 0.7464 (pt) cc_final: 0.6989 (mp) REVERT: x 673 ASN cc_start: 0.9235 (p0) cc_final: 0.9011 (p0) REVERT: x 700 THR cc_start: 0.9027 (p) cc_final: 0.8612 (p) outliers start: 5 outliers final: 1 residues processed: 2112 average time/residue: 1.4029 time to fit residues: 5106.3937 Evaluate side-chains 1719 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1718 time to evaluate : 5.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 817 optimal weight: 10.0000 chunk 557 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 731 optimal weight: 10.0000 chunk 405 optimal weight: 0.9980 chunk 838 optimal weight: 9.9990 chunk 678 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 501 optimal weight: 30.0000 chunk 881 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 62 ASN D 184 ASN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN ** J 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN K 45 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN ** W 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 HIS 2 4 ASN 2 26 ASN ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 118 ASN c 122 GLN d 137 GLN f 33 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 GLN ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 19 GLN o 83 ASN ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS ** t 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 68 HIS ** x 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 475 HIS ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 489 ASN ** x 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 159537 Z= 0.395 Angle : 0.817 14.653 238979 Z= 0.407 Chirality : 0.043 0.389 30585 Planarity : 0.006 0.109 12519 Dihedral : 25.329 179.569 80645 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 26.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.51 % Favored : 87.34 % Rotamer: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.96 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.11), residues: 5546 helix: -1.17 (0.12), residues: 1648 sheet: -1.37 (0.17), residues: 870 loop : -2.38 (0.11), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP b 96 HIS 0.016 0.002 HIS C 53 PHE 0.028 0.003 PHE q 75 TYR 0.030 0.002 TYR g 85 ARG 0.014 0.001 ARG N 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2005 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2004 time to evaluate : 6.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 SER cc_start: 0.8740 (p) cc_final: 0.8284 (m) REVERT: C 168 GLU cc_start: 0.7844 (mp0) cc_final: 0.7295 (tm-30) REVERT: D 83 LEU cc_start: 0.7357 (mt) cc_final: 0.7047 (mt) REVERT: D 100 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7590 (tm-30) REVERT: D 169 ILE cc_start: 0.8147 (mt) cc_final: 0.7822 (mt) REVERT: D 185 LEU cc_start: 0.9193 (mt) cc_final: 0.8798 (mp) REVERT: D 186 LEU cc_start: 0.9145 (mt) cc_final: 0.8696 (mt) REVERT: E 40 GLN cc_start: 0.8788 (tt0) cc_final: 0.8376 (tt0) REVERT: E 153 LEU cc_start: 0.8686 (tp) cc_final: 0.8482 (tp) REVERT: E 184 LEU cc_start: 0.9297 (pp) cc_final: 0.8773 (pp) REVERT: E 185 ASP cc_start: 0.8621 (m-30) cc_final: 0.7693 (m-30) REVERT: E 189 HIS cc_start: 0.7593 (m90) cc_final: 0.6436 (m90) REVERT: F 4 LEU cc_start: 0.8649 (tt) cc_final: 0.8448 (tt) REVERT: F 59 PHE cc_start: 0.8648 (m-80) cc_final: 0.8424 (m-80) REVERT: F 78 ARG cc_start: 0.7807 (ttm110) cc_final: 0.7598 (ttm110) REVERT: F 81 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7906 (mm-30) REVERT: F 118 SER cc_start: 0.9232 (t) cc_final: 0.9011 (p) REVERT: F 138 PHE cc_start: 0.7336 (p90) cc_final: 0.6865 (p90) REVERT: G 75 ASN cc_start: 0.8962 (m110) cc_final: 0.8533 (t0) REVERT: G 84 PHE cc_start: 0.8697 (m-80) cc_final: 0.8244 (m-80) REVERT: G 124 ILE cc_start: 0.8904 (mm) cc_final: 0.8539 (mm) REVERT: G 172 ARG cc_start: 0.8594 (mmp80) cc_final: 0.8199 (mmm160) REVERT: J 75 TYR cc_start: 0.8055 (m-10) cc_final: 0.6798 (m-10) REVERT: J 109 MET cc_start: 0.8654 (mtp) cc_final: 0.8364 (mtp) REVERT: J 119 MET cc_start: 0.8518 (mtm) cc_final: 0.8219 (mtp) REVERT: K 1 MET cc_start: 0.6762 (mmt) cc_final: 0.6260 (mmt) REVERT: K 2 ILE cc_start: 0.8415 (mt) cc_final: 0.8017 (mm) REVERT: K 25 LEU cc_start: 0.7568 (mm) cc_final: 0.7338 (mm) REVERT: K 54 LYS cc_start: 0.7940 (tttp) cc_final: 0.7399 (ttpt) REVERT: L 23 ILE cc_start: 0.7515 (pt) cc_final: 0.7104 (tp) REVERT: M 25 THR cc_start: 0.8877 (p) cc_final: 0.8657 (p) REVERT: M 32 PHE cc_start: 0.8061 (m-10) cc_final: 0.7414 (m-10) REVERT: M 44 ASN cc_start: 0.8873 (p0) cc_final: 0.8642 (p0) REVERT: M 57 TYR cc_start: 0.8560 (t80) cc_final: 0.8265 (t80) REVERT: M 59 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8836 (tptp) REVERT: M 103 LEU cc_start: 0.8865 (mt) cc_final: 0.8641 (mt) REVERT: M 113 VAL cc_start: 0.9336 (t) cc_final: 0.9041 (t) REVERT: M 124 LYS cc_start: 0.9208 (mmtm) cc_final: 0.8935 (mmmt) REVERT: M 128 LYS cc_start: 0.9006 (tttt) cc_final: 0.8418 (tttt) REVERT: N 38 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8737 (mtpp) REVERT: N 59 ARG cc_start: 0.8112 (tpp80) cc_final: 0.7829 (tpp80) REVERT: N 77 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8550 (tp-100) REVERT: N 81 GLN cc_start: 0.8528 (mt0) cc_final: 0.8174 (mt0) REVERT: N 82 LYS cc_start: 0.8784 (tttm) cc_final: 0.8123 (tttt) REVERT: N 95 GLN cc_start: 0.8434 (mt0) cc_final: 0.8014 (mp10) REVERT: N 118 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6834 (tm-30) REVERT: O 39 HIS cc_start: 0.7365 (m-70) cc_final: 0.6865 (m90) REVERT: P 5 ILE cc_start: 0.8337 (mm) cc_final: 0.8034 (mt) REVERT: P 13 LEU cc_start: 0.8983 (mt) cc_final: 0.8713 (mp) REVERT: P 84 ILE cc_start: 0.9382 (mm) cc_final: 0.9179 (mm) REVERT: Q 16 LYS cc_start: 0.8687 (tppt) cc_final: 0.8478 (tppt) REVERT: Q 32 TYR cc_start: 0.8713 (t80) cc_final: 0.8434 (t80) REVERT: Q 37 GLN cc_start: 0.7216 (mt0) cc_final: 0.6183 (tm-30) REVERT: Q 45 TYR cc_start: 0.8763 (m-10) cc_final: 0.7963 (m-10) REVERT: Q 89 GLU cc_start: 0.7778 (pm20) cc_final: 0.7546 (pm20) REVERT: R 69 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8422 (tppt) REVERT: S 62 TYR cc_start: 0.7590 (m-80) cc_final: 0.7021 (m-80) REVERT: S 68 ASN cc_start: 0.7803 (p0) cc_final: 0.7232 (p0) REVERT: S 70 VAL cc_start: 0.8662 (t) cc_final: 0.8399 (p) REVERT: S 96 ILE cc_start: 0.7997 (mm) cc_final: 0.7754 (tt) REVERT: S 106 VAL cc_start: 0.8605 (t) cc_final: 0.7611 (t) REVERT: T 13 ILE cc_start: 0.9186 (mp) cc_final: 0.8688 (tp) REVERT: T 21 MET cc_start: 0.8823 (mtm) cc_final: 0.8093 (mtt) REVERT: T 28 PHE cc_start: 0.8250 (m-80) cc_final: 0.7788 (m-80) REVERT: T 36 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8433 (mttt) REVERT: T 37 THR cc_start: 0.8745 (p) cc_final: 0.8485 (p) REVERT: T 46 ILE cc_start: 0.8849 (tp) cc_final: 0.8168 (tp) REVERT: T 57 MET cc_start: 0.7440 (mtp) cc_final: 0.6917 (mtp) REVERT: T 65 ARG cc_start: 0.7714 (tmm160) cc_final: 0.6571 (tmt170) REVERT: U 64 HIS cc_start: 0.8599 (t-90) cc_final: 0.7967 (t70) REVERT: U 75 THR cc_start: 0.8610 (p) cc_final: 0.8128 (p) REVERT: U 99 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8333 (mm-40) REVERT: X 15 GLU cc_start: 0.8525 (pm20) cc_final: 0.8190 (pm20) REVERT: X 18 VAL cc_start: 0.9361 (t) cc_final: 0.9048 (t) REVERT: Y 30 LYS cc_start: 0.8806 (mttt) cc_final: 0.8394 (mmmt) REVERT: Y 44 ARG cc_start: 0.8738 (tpp80) cc_final: 0.8154 (tpp80) REVERT: 1 21 LYS cc_start: 0.7460 (pttt) cc_final: 0.6416 (mmtm) REVERT: 1 27 MET cc_start: 0.7450 (mmm) cc_final: 0.7211 (mmm) REVERT: 2 29 ARG cc_start: 0.8538 (ttm170) cc_final: 0.8105 (mtt-85) REVERT: 2 30 VAL cc_start: 0.8878 (p) cc_final: 0.8582 (p) REVERT: 2 44 LEU cc_start: 0.8568 (tp) cc_final: 0.8361 (tt) REVERT: 2 47 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7082 (tm-30) REVERT: 3 1 MET cc_start: 0.5189 (mmm) cc_final: 0.4764 (mmp) REVERT: 4 23 LYS cc_start: 0.7406 (tmmt) cc_final: 0.6949 (pttp) REVERT: 4 56 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8419 (ttmm) REVERT: 5 1 MET cc_start: 0.8968 (tpp) cc_final: 0.8670 (tpp) REVERT: 5 4 ARG cc_start: 0.8199 (ptp-170) cc_final: 0.7879 (ptm160) REVERT: Z 1 MET cc_start: 0.8692 (tpp) cc_final: 0.8473 (tpp) REVERT: b 45 LYS cc_start: 0.9493 (mtmt) cc_final: 0.9229 (mtmt) REVERT: b 108 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8845 (mm110) REVERT: b 137 LEU cc_start: 0.8510 (tp) cc_final: 0.8297 (tp) REVERT: b 141 LEU cc_start: 0.9589 (mt) cc_final: 0.9371 (mt) REVERT: b 144 LEU cc_start: 0.8966 (mm) cc_final: 0.8755 (mm) REVERT: b 177 ARG cc_start: 0.8228 (ttt90) cc_final: 0.8001 (ttt90) REVERT: b 178 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7990 (tptp) REVERT: b 184 ILE cc_start: 0.8928 (pt) cc_final: 0.8626 (pt) REVERT: c 31 PHE cc_start: 0.8492 (m-80) cc_final: 0.7948 (m-80) REVERT: c 182 ASP cc_start: 0.7988 (t70) cc_final: 0.7665 (t0) REVERT: d 47 TYR cc_start: 0.8462 (t80) cc_final: 0.7982 (t80) REVERT: d 50 GLN cc_start: 0.9300 (mt0) cc_final: 0.8490 (mm-40) REVERT: d 59 HIS cc_start: 0.8232 (m-70) cc_final: 0.7681 (m-70) REVERT: d 67 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7462 (tp40) REVERT: d 198 TYR cc_start: 0.8225 (m-80) cc_final: 0.7788 (m-10) REVERT: e 20 ARG cc_start: 0.7374 (ttm110) cc_final: 0.7056 (ttp-110) REVERT: e 76 MET cc_start: 0.6961 (mmt) cc_final: 0.6639 (mmp) REVERT: e 88 ARG cc_start: 0.7486 (mtt-85) cc_final: 0.7001 (mmt180) REVERT: e 93 ASN cc_start: 0.8150 (m-40) cc_final: 0.5782 (t0) REVERT: e 147 LEU cc_start: 0.9061 (mt) cc_final: 0.8535 (mt) REVERT: e 152 ASP cc_start: 0.9082 (m-30) cc_final: 0.8842 (m-30) REVERT: f 5 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7063 (tm-30) REVERT: f 7 MET cc_start: 0.8322 (tpt) cc_final: 0.8084 (tpt) REVERT: f 19 LYS cc_start: 0.8799 (mtmm) cc_final: 0.7770 (mttm) REVERT: f 48 LEU cc_start: 0.9043 (mt) cc_final: 0.8796 (mt) REVERT: f 54 ASP cc_start: 0.8003 (p0) cc_final: 0.7583 (p0) REVERT: f 61 GLN cc_start: 0.8336 (mp10) cc_final: 0.7704 (mp10) REVERT: f 62 ILE cc_start: 0.8168 (mp) cc_final: 0.7366 (mp) REVERT: g 17 ILE cc_start: 0.8946 (pt) cc_final: 0.8064 (pt) REVERT: g 28 ASN cc_start: 0.8820 (m-40) cc_final: 0.8564 (m-40) REVERT: g 31 MET cc_start: 0.9033 (ttm) cc_final: 0.8298 (ttt) REVERT: g 49 ILE cc_start: 0.9173 (pt) cc_final: 0.8856 (pt) REVERT: g 60 GLU cc_start: 0.8068 (pm20) cc_final: 0.7722 (pm20) REVERT: g 61 VAL cc_start: 0.9241 (t) cc_final: 0.8895 (t) REVERT: g 68 ASN cc_start: 0.9402 (m-40) cc_final: 0.9088 (m-40) REVERT: g 80 VAL cc_start: 0.8517 (p) cc_final: 0.8187 (m) REVERT: g 122 ASN cc_start: 0.8842 (m-40) cc_final: 0.8514 (m110) REVERT: g 130 ASN cc_start: 0.8648 (p0) cc_final: 0.8067 (p0) REVERT: h 39 ILE cc_start: 0.8891 (mm) cc_final: 0.8123 (mm) REVERT: h 41 LYS cc_start: 0.9176 (tptm) cc_final: 0.8957 (tptm) REVERT: h 66 TYR cc_start: 0.8167 (m-10) cc_final: 0.7957 (m-80) REVERT: h 98 LEU cc_start: 0.9185 (mt) cc_final: 0.8626 (mm) REVERT: h 101 LEU cc_start: 0.9044 (tt) cc_final: 0.8811 (tt) REVERT: i 25 GLU cc_start: 0.7085 (pp20) cc_final: 0.6783 (pp20) REVERT: i 81 HIS cc_start: 0.8250 (t70) cc_final: 0.7945 (t-90) REVERT: j 53 ARG cc_start: 0.8782 (ttm170) cc_final: 0.7884 (ttm170) REVERT: j 61 SER cc_start: 0.8946 (p) cc_final: 0.8647 (p) REVERT: j 63 GLU cc_start: 0.7911 (tt0) cc_final: 0.7639 (tt0) REVERT: j 90 LEU cc_start: 0.9226 (mt) cc_final: 0.8902 (mt) REVERT: k 31 ASN cc_start: 0.8648 (t0) cc_final: 0.8356 (t0) REVERT: k 36 ILE cc_start: 0.9178 (pt) cc_final: 0.8928 (pt) REVERT: k 54 PHE cc_start: 0.7868 (m-80) cc_final: 0.7641 (m-80) REVERT: k 83 THR cc_start: 0.9267 (p) cc_final: 0.8977 (p) REVERT: k 88 VAL cc_start: 0.9403 (t) cc_final: 0.8964 (m) REVERT: k 128 ARG cc_start: 0.8260 (ttm170) cc_final: 0.8034 (mtp180) REVERT: l 24 LEU cc_start: 0.9270 (mt) cc_final: 0.9049 (mt) REVERT: l 35 HIS cc_start: 0.7757 (m-70) cc_final: 0.7217 (m90) REVERT: l 128 SER cc_start: 0.8714 (p) cc_final: 0.8488 (p) REVERT: m 31 GLN cc_start: 0.9264 (mt0) cc_final: 0.8812 (mt0) REVERT: m 76 ASN cc_start: 0.9201 (m-40) cc_final: 0.8932 (m110) REVERT: m 87 ARG cc_start: 0.9008 (ttp80) cc_final: 0.8440 (ttt90) REVERT: m 100 GLN cc_start: 0.8905 (mp10) cc_final: 0.8614 (mp10) REVERT: n 17 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8441 (tptp) REVERT: n 23 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7438 (mmt90) REVERT: n 42 ILE cc_start: 0.9289 (mt) cc_final: 0.9040 (tp) REVERT: o 43 LEU cc_start: 0.9264 (mp) cc_final: 0.8802 (mt) REVERT: o 62 LYS cc_start: 0.8867 (mttt) cc_final: 0.8616 (mmmt) REVERT: p 6 ARG cc_start: 0.9084 (ptt180) cc_final: 0.8405 (ptt90) REVERT: p 65 LYS cc_start: 0.8826 (mttt) cc_final: 0.8470 (mttm) REVERT: p 79 ILE cc_start: 0.8758 (mp) cc_final: 0.8475 (mp) REVERT: q 19 MET cc_start: 0.7529 (mpp) cc_final: 0.7196 (mmp) REVERT: q 27 VAL cc_start: 0.8669 (t) cc_final: 0.8203 (m) REVERT: q 41 LYS cc_start: 0.8898 (pttt) cc_final: 0.8164 (ptpp) REVERT: q 56 LYS cc_start: 0.8078 (mttt) cc_final: 0.7747 (mmtt) REVERT: r 33 LEU cc_start: 0.9398 (mt) cc_final: 0.8786 (tp) REVERT: r 36 LYS cc_start: 0.9332 (mtmm) cc_final: 0.9034 (mttp) REVERT: r 43 LYS cc_start: 0.8382 (mtmm) cc_final: 0.7983 (mttp) REVERT: r 45 LEU cc_start: 0.9037 (mt) cc_final: 0.8565 (mt) REVERT: r 48 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7632 (mtt180) REVERT: s 43 GLN cc_start: 0.9530 (pm20) cc_final: 0.9320 (pm20) REVERT: s 49 ILE cc_start: 0.9220 (tp) cc_final: 0.9017 (mp) REVERT: t 49 THR cc_start: 0.9738 (p) cc_final: 0.9367 (p) REVERT: t 60 LYS cc_start: 0.9014 (mttt) cc_final: 0.8186 (ttmm) REVERT: t 70 ASN cc_start: 0.8938 (m110) cc_final: 0.8541 (t0) REVERT: x 395 TYR cc_start: 0.7423 (m-80) cc_final: 0.7201 (m-10) REVERT: x 464 TRP cc_start: 0.8406 (m-90) cc_final: 0.7930 (m-10) REVERT: x 595 LEU cc_start: 0.9303 (mt) cc_final: 0.9070 (mt) REVERT: x 658 ASN cc_start: 0.8639 (m-40) cc_final: 0.8255 (m110) REVERT: x 673 ASN cc_start: 0.9199 (p0) cc_final: 0.8994 (p0) REVERT: x 700 THR cc_start: 0.9048 (p) cc_final: 0.8517 (p) outliers start: 1 outliers final: 0 residues processed: 2005 average time/residue: 1.3047 time to fit residues: 4476.0978 Evaluate side-chains 1672 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1672 time to evaluate : 6.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 330 optimal weight: 4.9990 chunk 884 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 576 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 983 optimal weight: 6.9990 chunk 816 optimal weight: 2.9990 chunk 455 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 325 optimal weight: 6.9990 chunk 516 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 62 ASN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 HIS Q 36 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN ** W 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 HIS ** 1 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 HIS ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 122 GLN d 52 GLN f 33 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 HIS ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS m 32 GLN ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS t 68 HIS x 475 HIS x 479 GLN ** x 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 159537 Z= 0.234 Angle : 0.677 14.512 238979 Z= 0.346 Chirality : 0.038 0.395 30585 Planarity : 0.005 0.104 12519 Dihedral : 25.190 179.755 80645 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.44 % Favored : 89.43 % Rotamer: Outliers : 0.02 % Allowed : 2.30 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.96 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.11), residues: 5546 helix: -0.97 (0.12), residues: 1656 sheet: -1.23 (0.17), residues: 859 loop : -2.29 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP b 96 HIS 0.010 0.001 HIS f 88 PHE 0.023 0.002 PHE M 104 TYR 0.024 0.002 TYR f 60 ARG 0.009 0.001 ARG X 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2007 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2006 time to evaluate : 6.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 SER cc_start: 0.8655 (p) cc_final: 0.8128 (m) REVERT: C 115 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7515 (tm-30) REVERT: C 116 ILE cc_start: 0.8895 (mt) cc_final: 0.8677 (mt) REVERT: C 168 GLU cc_start: 0.7680 (mp0) cc_final: 0.7288 (tm-30) REVERT: D 84 ARG cc_start: 0.7137 (tpp80) cc_final: 0.6497 (ttt180) REVERT: D 100 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7565 (tm-30) REVERT: D 185 LEU cc_start: 0.9137 (mt) cc_final: 0.8769 (mp) REVERT: D 186 LEU cc_start: 0.9148 (mt) cc_final: 0.8729 (mt) REVERT: E 40 GLN cc_start: 0.8779 (tt0) cc_final: 0.8388 (tt0) REVERT: E 160 ASN cc_start: 0.8473 (m110) cc_final: 0.8258 (m-40) REVERT: E 165 LEU cc_start: 0.9264 (mt) cc_final: 0.8735 (tp) REVERT: E 184 LEU cc_start: 0.9259 (pp) cc_final: 0.8738 (pp) REVERT: E 185 ASP cc_start: 0.8700 (m-30) cc_final: 0.7919 (m-30) REVERT: E 189 HIS cc_start: 0.7461 (m90) cc_final: 0.5946 (m90) REVERT: F 154 ILE cc_start: 0.8342 (mm) cc_final: 0.8115 (mm) REVERT: F 170 LEU cc_start: 0.8904 (mt) cc_final: 0.8457 (mt) REVERT: G 75 ASN cc_start: 0.8909 (m110) cc_final: 0.8482 (t0) REVERT: G 172 ARG cc_start: 0.8653 (mmp80) cc_final: 0.8219 (mmm160) REVERT: J 50 ASP cc_start: 0.7890 (t70) cc_final: 0.5129 (t70) REVERT: J 109 MET cc_start: 0.8551 (mtp) cc_final: 0.8258 (mtp) REVERT: J 119 MET cc_start: 0.8354 (mtm) cc_final: 0.7588 (mmm) REVERT: K 1 MET cc_start: 0.6641 (mmt) cc_final: 0.6208 (mmt) REVERT: K 2 ILE cc_start: 0.8509 (mt) cc_final: 0.8137 (mm) REVERT: K 5 GLU cc_start: 0.8626 (mp0) cc_final: 0.7992 (mp0) REVERT: K 54 LYS cc_start: 0.7962 (tttp) cc_final: 0.7446 (ttpt) REVERT: L 23 ILE cc_start: 0.7472 (pt) cc_final: 0.7031 (tp) REVERT: M 32 PHE cc_start: 0.7849 (m-10) cc_final: 0.7291 (m-10) REVERT: M 41 TRP cc_start: 0.8773 (m-10) cc_final: 0.8523 (m-10) REVERT: M 44 ASN cc_start: 0.8735 (p0) cc_final: 0.8450 (p0) REVERT: M 59 LYS cc_start: 0.9124 (tmtt) cc_final: 0.8879 (tptp) REVERT: M 103 LEU cc_start: 0.8949 (mt) cc_final: 0.8687 (mm) REVERT: M 124 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8853 (mmmt) REVERT: M 128 LYS cc_start: 0.8968 (tttt) cc_final: 0.8207 (tttt) REVERT: N 59 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7780 (tpp80) REVERT: N 77 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8726 (tp-100) REVERT: N 81 GLN cc_start: 0.8417 (mt0) cc_final: 0.7994 (mt0) REVERT: N 82 LYS cc_start: 0.8758 (tttm) cc_final: 0.8129 (tttt) REVERT: N 95 GLN cc_start: 0.8231 (mt0) cc_final: 0.7875 (mp10) REVERT: N 118 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6527 (tm-30) REVERT: O 15 HIS cc_start: 0.8222 (t70) cc_final: 0.7886 (t70) REVERT: O 44 ILE cc_start: 0.8631 (mp) cc_final: 0.8386 (mp) REVERT: O 118 LEU cc_start: 0.9173 (mm) cc_final: 0.8899 (mm) REVERT: P 5 ILE cc_start: 0.8420 (mm) cc_final: 0.8220 (mt) REVERT: P 13 LEU cc_start: 0.8888 (mt) cc_final: 0.8462 (mp) REVERT: P 84 ILE cc_start: 0.8938 (mm) cc_final: 0.8550 (mm) REVERT: Q 37 GLN cc_start: 0.7321 (mt0) cc_final: 0.6115 (tm-30) REVERT: Q 45 TYR cc_start: 0.8585 (m-10) cc_final: 0.7819 (m-10) REVERT: Q 59 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7563 (ttmt) REVERT: Q 61 TRP cc_start: 0.9102 (m-10) cc_final: 0.8868 (m-10) REVERT: Q 63 THR cc_start: 0.9117 (m) cc_final: 0.8903 (t) REVERT: R 69 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8393 (tppt) REVERT: S 62 TYR cc_start: 0.7556 (m-80) cc_final: 0.7250 (m-80) REVERT: S 65 ASP cc_start: 0.8581 (t0) cc_final: 0.8030 (t70) REVERT: S 84 ARG cc_start: 0.6563 (mpt180) cc_final: 0.5405 (tpt170) REVERT: S 106 VAL cc_start: 0.8418 (t) cc_final: 0.7426 (t) REVERT: T 13 ILE cc_start: 0.9192 (mp) cc_final: 0.8718 (tp) REVERT: T 21 MET cc_start: 0.8840 (mtm) cc_final: 0.8132 (mtt) REVERT: T 28 PHE cc_start: 0.8045 (m-80) cc_final: 0.7672 (m-80) REVERT: T 37 THR cc_start: 0.8643 (p) cc_final: 0.8441 (p) REVERT: T 46 ILE cc_start: 0.8970 (tp) cc_final: 0.8510 (tp) REVERT: T 57 MET cc_start: 0.7361 (mtp) cc_final: 0.6879 (mtp) REVERT: T 65 ARG cc_start: 0.7610 (tmm160) cc_final: 0.6188 (tmt170) REVERT: U 56 ILE cc_start: 0.8664 (mm) cc_final: 0.8351 (tp) REVERT: U 64 HIS cc_start: 0.8581 (t-90) cc_final: 0.8008 (t70) REVERT: U 99 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8332 (mm-40) REVERT: V 22 ARG cc_start: 0.7444 (pmt170) cc_final: 0.6999 (ptt-90) REVERT: V 29 LEU cc_start: 0.9235 (mt) cc_final: 0.8866 (mt) REVERT: W 22 MET cc_start: 0.0350 (mtm) cc_final: 0.0094 (mtm) REVERT: X 22 LYS cc_start: 0.8949 (tttt) cc_final: 0.8250 (mmmm) REVERT: X 24 GLU cc_start: 0.8497 (pt0) cc_final: 0.8225 (pt0) REVERT: X 28 LEU cc_start: 0.9173 (mm) cc_final: 0.8895 (tp) REVERT: X 43 ILE cc_start: 0.9291 (mp) cc_final: 0.9039 (mp) REVERT: X 52 ARG cc_start: 0.8713 (ptm160) cc_final: 0.8383 (ptm160) REVERT: Y 30 LYS cc_start: 0.8762 (mttt) cc_final: 0.8358 (mmmt) REVERT: 1 21 LYS cc_start: 0.7262 (pttt) cc_final: 0.6350 (mmtm) REVERT: 1 27 MET cc_start: 0.7533 (mmm) cc_final: 0.7240 (mmm) REVERT: 2 25 ASN cc_start: 0.8641 (m110) cc_final: 0.8346 (m-40) REVERT: 2 30 VAL cc_start: 0.8798 (p) cc_final: 0.8523 (p) REVERT: 3 1 MET cc_start: 0.4945 (mmm) cc_final: 0.4530 (mmp) REVERT: 3 11 LYS cc_start: 0.8415 (mttt) cc_final: 0.8180 (mttp) REVERT: 3 14 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8452 (mmtm) REVERT: 4 23 LYS cc_start: 0.7218 (tmmt) cc_final: 0.6769 (pttp) REVERT: 4 56 LYS cc_start: 0.8929 (ttpp) cc_final: 0.8396 (ttmm) REVERT: 5 1 MET cc_start: 0.8956 (tpp) cc_final: 0.8546 (tpp) REVERT: 5 4 ARG cc_start: 0.8136 (ptp-170) cc_final: 0.7873 (ptm160) REVERT: 5 34 GLN cc_start: 0.8266 (mt0) cc_final: 0.7898 (tt0) REVERT: Z 1 MET cc_start: 0.8737 (tpp) cc_final: 0.8535 (tpp) REVERT: Z 10 LYS cc_start: 0.7439 (pttm) cc_final: 0.6678 (mtmm) REVERT: Z 13 THR cc_start: 0.8719 (p) cc_final: 0.8501 (t) REVERT: Z 28 LYS cc_start: 0.7276 (tmmt) cc_final: 0.6981 (tmmt) REVERT: b 45 LYS cc_start: 0.9482 (mtmt) cc_final: 0.9189 (mtmt) REVERT: b 177 ARG cc_start: 0.8300 (ttt90) cc_final: 0.8058 (ttt90) REVERT: b 178 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7942 (tptp) REVERT: c 31 PHE cc_start: 0.8544 (m-80) cc_final: 0.8083 (m-80) REVERT: c 88 LYS cc_start: 0.9304 (ptpp) cc_final: 0.8938 (pttm) REVERT: c 101 ASN cc_start: 0.8196 (t0) cc_final: 0.7988 (t0) REVERT: d 47 TYR cc_start: 0.8503 (t80) cc_final: 0.8063 (t80) REVERT: d 50 GLN cc_start: 0.9347 (mt0) cc_final: 0.8576 (mm-40) REVERT: d 59 HIS cc_start: 0.8182 (m-70) cc_final: 0.7563 (m-70) REVERT: d 87 MET cc_start: 0.8553 (mtm) cc_final: 0.7951 (mtp) REVERT: d 196 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6965 (mt-10) REVERT: d 198 TYR cc_start: 0.8196 (m-80) cc_final: 0.7707 (m-10) REVERT: e 20 ARG cc_start: 0.7323 (ttm110) cc_final: 0.7115 (ttp-170) REVERT: e 61 ARG cc_start: 0.9060 (ttp-110) cc_final: 0.8768 (ttm110) REVERT: e 65 GLU cc_start: 0.7928 (tt0) cc_final: 0.7679 (tp30) REVERT: e 76 MET cc_start: 0.7107 (mmt) cc_final: 0.6536 (mmp) REVERT: e 88 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.6953 (mmt180) REVERT: e 93 ASN cc_start: 0.8133 (m-40) cc_final: 0.5963 (t0) REVERT: e 123 ILE cc_start: 0.8971 (mp) cc_final: 0.8771 (mp) REVERT: e 141 LEU cc_start: 0.9292 (mm) cc_final: 0.8661 (tt) REVERT: e 144 LEU cc_start: 0.9114 (mt) cc_final: 0.8892 (mt) REVERT: e 147 LEU cc_start: 0.9003 (mt) cc_final: 0.8559 (mt) REVERT: e 152 ASP cc_start: 0.9002 (m-30) cc_final: 0.8699 (m-30) REVERT: f 5 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7420 (tm-30) REVERT: f 19 LYS cc_start: 0.8972 (mtmm) cc_final: 0.7969 (mttm) REVERT: f 91 VAL cc_start: 0.8863 (t) cc_final: 0.8633 (t) REVERT: g 17 ILE cc_start: 0.8796 (pt) cc_final: 0.7836 (pt) REVERT: g 28 ASN cc_start: 0.8721 (m-40) cc_final: 0.8444 (m-40) REVERT: g 31 MET cc_start: 0.9009 (ttm) cc_final: 0.8339 (ttt) REVERT: g 57 ASP cc_start: 0.8058 (m-30) cc_final: 0.7832 (t70) REVERT: g 59 MET cc_start: 0.8970 (mmm) cc_final: 0.8640 (mmm) REVERT: g 61 VAL cc_start: 0.9152 (t) cc_final: 0.8910 (t) REVERT: g 68 ASN cc_start: 0.9354 (m-40) cc_final: 0.8995 (m-40) REVERT: g 80 VAL cc_start: 0.8551 (p) cc_final: 0.7924 (m) REVERT: g 122 ASN cc_start: 0.8786 (m-40) cc_final: 0.8447 (m110) REVERT: g 130 ASN cc_start: 0.8569 (p0) cc_final: 0.7932 (p0) REVERT: h 39 ILE cc_start: 0.8951 (mm) cc_final: 0.8197 (mm) REVERT: h 66 TYR cc_start: 0.8071 (m-10) cc_final: 0.7871 (m-80) REVERT: h 98 LEU cc_start: 0.9133 (mt) cc_final: 0.8625 (mm) REVERT: h 101 LEU cc_start: 0.9133 (tt) cc_final: 0.8916 (tt) REVERT: h 126 GLU cc_start: 0.8424 (tp30) cc_final: 0.8011 (tp30) REVERT: h 127 VAL cc_start: 0.9126 (t) cc_final: 0.8587 (t) REVERT: i 34 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7561 (mm-30) REVERT: i 103 LEU cc_start: 0.8651 (mt) cc_final: 0.8245 (mt) REVERT: j 10 LEU cc_start: 0.9033 (mm) cc_final: 0.8800 (mm) REVERT: j 53 ARG cc_start: 0.8759 (ttm170) cc_final: 0.7776 (ttt180) REVERT: j 61 SER cc_start: 0.8969 (p) cc_final: 0.8652 (p) REVERT: j 68 ARG cc_start: 0.8257 (mtt90) cc_final: 0.7944 (mtt90) REVERT: j 90 LEU cc_start: 0.9236 (mt) cc_final: 0.8926 (mt) REVERT: k 54 PHE cc_start: 0.7929 (m-80) cc_final: 0.7629 (m-80) REVERT: k 83 THR cc_start: 0.9236 (p) cc_final: 0.8875 (p) REVERT: k 88 VAL cc_start: 0.9421 (t) cc_final: 0.9096 (m) REVERT: l 35 HIS cc_start: 0.7745 (m-70) cc_final: 0.7144 (m90) REVERT: l 128 SER cc_start: 0.8737 (p) cc_final: 0.8527 (p) REVERT: m 87 ARG cc_start: 0.8985 (ttp80) cc_final: 0.8263 (ttt90) REVERT: m 100 GLN cc_start: 0.8890 (mp10) cc_final: 0.8641 (mp10) REVERT: n 6 MET cc_start: 0.8470 (tpp) cc_final: 0.7880 (tpp) REVERT: n 21 TYR cc_start: 0.8498 (p90) cc_final: 0.7629 (p90) REVERT: n 39 LEU cc_start: 0.9052 (mt) cc_final: 0.8427 (tp) REVERT: n 42 ILE cc_start: 0.9280 (mt) cc_final: 0.9006 (tp) REVERT: n 58 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8539 (mmmm) REVERT: o 7 ARG cc_start: 0.8748 (tpt90) cc_final: 0.7973 (tpt90) REVERT: o 11 LEU cc_start: 0.9263 (mt) cc_final: 0.8834 (mt) REVERT: o 62 LYS cc_start: 0.8812 (mttt) cc_final: 0.8490 (mmmt) REVERT: o 70 LEU cc_start: 0.9263 (tp) cc_final: 0.8515 (tp) REVERT: p 6 ARG cc_start: 0.8977 (ptt180) cc_final: 0.8334 (ptt90) REVERT: p 65 LYS cc_start: 0.8835 (mttt) cc_final: 0.8565 (mttm) REVERT: p 79 ILE cc_start: 0.8859 (mp) cc_final: 0.8514 (mp) REVERT: p 80 MET cc_start: 0.8238 (mmm) cc_final: 0.7986 (mmm) REVERT: p 83 PHE cc_start: 0.8859 (t80) cc_final: 0.8518 (t80) REVERT: q 19 MET cc_start: 0.7564 (mpp) cc_final: 0.7208 (mmp) REVERT: q 27 VAL cc_start: 0.8674 (t) cc_final: 0.8209 (m) REVERT: q 41 LYS cc_start: 0.8821 (pttt) cc_final: 0.8094 (ptpp) REVERT: q 56 LYS cc_start: 0.8053 (mttt) cc_final: 0.7769 (mmtt) REVERT: r 33 LEU cc_start: 0.9421 (mt) cc_final: 0.8900 (tp) REVERT: r 36 LYS cc_start: 0.9295 (mtmm) cc_final: 0.8961 (mttp) REVERT: r 43 LYS cc_start: 0.8350 (mtmm) cc_final: 0.7962 (mttp) REVERT: r 45 LEU cc_start: 0.8971 (mt) cc_final: 0.8493 (mt) REVERT: r 48 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7606 (mtt180) REVERT: r 75 TYR cc_start: 0.8255 (m-80) cc_final: 0.7470 (m-10) REVERT: t 59 ASP cc_start: 0.8372 (m-30) cc_final: 0.8171 (m-30) REVERT: t 60 LYS cc_start: 0.8875 (mttt) cc_final: 0.8040 (ttmm) REVERT: t 70 ASN cc_start: 0.8977 (m110) cc_final: 0.8715 (p0) REVERT: x 395 TYR cc_start: 0.7386 (m-80) cc_final: 0.7168 (m-10) REVERT: x 464 TRP cc_start: 0.8229 (m-90) cc_final: 0.7726 (m-10) REVERT: x 595 LEU cc_start: 0.9318 (mt) cc_final: 0.9078 (mt) REVERT: x 658 ASN cc_start: 0.8559 (m-40) cc_final: 0.8195 (m110) REVERT: x 719 ARG cc_start: 0.6347 (tpt170) cc_final: 0.6102 (tpt-90) outliers start: 1 outliers final: 0 residues processed: 2007 average time/residue: 1.3154 time to fit residues: 4535.3357 Evaluate side-chains 1693 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1693 time to evaluate : 5.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 947 optimal weight: 30.0000 chunk 110 optimal weight: 50.0000 chunk 560 optimal weight: 3.9990 chunk 717 optimal weight: 20.0000 chunk 556 optimal weight: 0.8980 chunk 827 optimal weight: 9.9990 chunk 548 optimal weight: 1.9990 chunk 979 optimal weight: 20.0000 chunk 612 optimal weight: 20.0000 chunk 597 optimal weight: 50.0000 chunk 452 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 62 ASN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS U 58 ASN ** W 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 HIS 2 4 ASN ** 2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 85 GLN c 68 HIS c 118 ASN c 122 GLN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 HIS ** d 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 5 GLN ** i 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS ** t 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 159537 Z= 0.270 Angle : 0.704 14.583 238979 Z= 0.358 Chirality : 0.039 0.388 30585 Planarity : 0.006 0.118 12519 Dihedral : 25.201 179.226 80645 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.50 % Favored : 88.37 % Rotamer: Outliers : 0.08 % Allowed : 1.94 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.96 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.11), residues: 5546 helix: -0.94 (0.12), residues: 1660 sheet: -1.19 (0.17), residues: 883 loop : -2.35 (0.11), residues: 3003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP b 96 HIS 0.014 0.002 HIS t 68 PHE 0.024 0.002 PHE q 75 TYR 0.026 0.002 TYR g 85 ARG 0.014 0.001 ARG j 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1966 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1962 time to evaluate : 6.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 SER cc_start: 0.8660 (p) cc_final: 0.8175 (m) REVERT: C 115 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7507 (tm-30) REVERT: C 116 ILE cc_start: 0.8895 (mt) cc_final: 0.8671 (mt) REVERT: C 168 GLU cc_start: 0.7776 (mp0) cc_final: 0.7374 (tm-30) REVERT: D 16 PHE cc_start: 0.6763 (m-80) cc_final: 0.6400 (m-10) REVERT: D 100 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7555 (tm-30) REVERT: D 185 LEU cc_start: 0.9130 (mt) cc_final: 0.8768 (mp) REVERT: D 186 LEU cc_start: 0.9166 (mt) cc_final: 0.8757 (mt) REVERT: E 40 GLN cc_start: 0.8797 (tt0) cc_final: 0.8407 (tt0) REVERT: E 153 LEU cc_start: 0.8613 (tp) cc_final: 0.8173 (tp) REVERT: E 161 GLU cc_start: 0.8411 (pp20) cc_final: 0.8124 (pp20) REVERT: E 165 LEU cc_start: 0.9237 (mt) cc_final: 0.8821 (tp) REVERT: E 184 LEU cc_start: 0.9300 (pp) cc_final: 0.8758 (pp) REVERT: E 185 ASP cc_start: 0.8764 (m-30) cc_final: 0.7605 (m-30) REVERT: E 189 HIS cc_start: 0.7391 (m90) cc_final: 0.5814 (m90) REVERT: F 170 LEU cc_start: 0.8892 (mt) cc_final: 0.8492 (mt) REVERT: G 75 ASN cc_start: 0.8908 (m110) cc_final: 0.8559 (t0) REVERT: G 84 PHE cc_start: 0.8625 (m-80) cc_final: 0.8350 (m-80) REVERT: G 172 ARG cc_start: 0.8678 (mmp80) cc_final: 0.8186 (mmm160) REVERT: J 14 ARG cc_start: 0.6879 (mmm-85) cc_final: 0.6605 (mtt180) REVERT: J 50 ASP cc_start: 0.8059 (t70) cc_final: 0.5675 (t0) REVERT: J 109 MET cc_start: 0.8575 (mtp) cc_final: 0.8314 (mtp) REVERT: J 119 MET cc_start: 0.8302 (mtm) cc_final: 0.7755 (mmm) REVERT: K 1 MET cc_start: 0.6797 (mmt) cc_final: 0.6376 (mmt) REVERT: K 2 ILE cc_start: 0.8496 (mt) cc_final: 0.8131 (mm) REVERT: K 5 GLU cc_start: 0.8642 (mp0) cc_final: 0.7991 (mp0) REVERT: K 54 LYS cc_start: 0.8021 (tttp) cc_final: 0.7604 (ttpt) REVERT: L 23 ILE cc_start: 0.7611 (pt) cc_final: 0.7126 (tp) REVERT: M 25 THR cc_start: 0.8918 (p) cc_final: 0.8653 (p) REVERT: M 32 PHE cc_start: 0.7920 (m-10) cc_final: 0.7338 (m-10) REVERT: M 44 ASN cc_start: 0.8699 (p0) cc_final: 0.8383 (p0) REVERT: M 59 LYS cc_start: 0.9170 (tmtt) cc_final: 0.8880 (tptp) REVERT: M 74 TYR cc_start: 0.7953 (p90) cc_final: 0.7672 (p90) REVERT: M 124 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8887 (mmmt) REVERT: M 128 LYS cc_start: 0.8978 (tttt) cc_final: 0.8245 (tttp) REVERT: N 59 ARG cc_start: 0.8267 (tpp80) cc_final: 0.7763 (tpp80) REVERT: N 81 GLN cc_start: 0.8412 (mt0) cc_final: 0.8010 (mt0) REVERT: N 82 LYS cc_start: 0.8780 (tttm) cc_final: 0.8141 (tttt) REVERT: N 83 LEU cc_start: 0.9427 (tp) cc_final: 0.9196 (tp) REVERT: N 95 GLN cc_start: 0.8342 (mt0) cc_final: 0.8001 (mp10) REVERT: N 116 ILE cc_start: 0.8523 (mt) cc_final: 0.8138 (mt) REVERT: N 118 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6711 (tm-30) REVERT: O 15 HIS cc_start: 0.8244 (t70) cc_final: 0.7851 (t70) REVERT: O 44 ILE cc_start: 0.8701 (mp) cc_final: 0.8399 (mm) REVERT: O 118 LEU cc_start: 0.9162 (mm) cc_final: 0.8892 (mm) REVERT: P 101 ARG cc_start: 0.7391 (mtt180) cc_final: 0.6948 (mmt90) REVERT: Q 37 GLN cc_start: 0.7481 (mt0) cc_final: 0.6218 (tm-30) REVERT: Q 45 TYR cc_start: 0.8621 (m-10) cc_final: 0.7815 (m-10) REVERT: Q 49 ASP cc_start: 0.8041 (m-30) cc_final: 0.7712 (m-30) REVERT: Q 50 ARG cc_start: 0.8404 (ptp-110) cc_final: 0.8104 (ptp-110) REVERT: Q 59 LYS cc_start: 0.7795 (ttmt) cc_final: 0.7569 (ttmt) REVERT: Q 61 TRP cc_start: 0.9129 (m-10) cc_final: 0.8880 (m-10) REVERT: Q 63 THR cc_start: 0.9126 (m) cc_final: 0.8910 (t) REVERT: Q 116 GLN cc_start: 0.8019 (tp40) cc_final: 0.7812 (tp40) REVERT: R 69 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8385 (tppt) REVERT: S 106 VAL cc_start: 0.8457 (t) cc_final: 0.7439 (t) REVERT: T 3 ASP cc_start: 0.8604 (p0) cc_final: 0.8231 (p0) REVERT: T 13 ILE cc_start: 0.9207 (mp) cc_final: 0.8711 (tp) REVERT: T 21 MET cc_start: 0.8839 (mtm) cc_final: 0.8042 (mtt) REVERT: T 28 PHE cc_start: 0.8041 (m-80) cc_final: 0.7705 (m-80) REVERT: T 37 THR cc_start: 0.8754 (p) cc_final: 0.8541 (p) REVERT: T 46 ILE cc_start: 0.8875 (tp) cc_final: 0.8652 (tp) REVERT: T 57 MET cc_start: 0.7206 (mtp) cc_final: 0.6660 (mtp) REVERT: U 1 MET cc_start: 0.7390 (mtt) cc_final: 0.7063 (mtm) REVERT: U 56 ILE cc_start: 0.8660 (mm) cc_final: 0.8449 (tp) REVERT: U 64 HIS cc_start: 0.8599 (t-90) cc_final: 0.7754 (t-170) REVERT: U 99 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8409 (mm-40) REVERT: V 46 TYR cc_start: 0.7847 (t80) cc_final: 0.7632 (t80) REVERT: W 47 VAL cc_start: 0.6455 (t) cc_final: 0.6193 (m) REVERT: X 24 GLU cc_start: 0.8507 (pt0) cc_final: 0.8260 (pt0) REVERT: X 28 LEU cc_start: 0.9181 (mm) cc_final: 0.8953 (tp) REVERT: X 43 ILE cc_start: 0.9263 (mp) cc_final: 0.9057 (mp) REVERT: X 52 ARG cc_start: 0.8855 (ptm160) cc_final: 0.8431 (ptm-80) REVERT: Y 30 LYS cc_start: 0.8779 (mttt) cc_final: 0.8366 (mmmt) REVERT: Y 38 GLU cc_start: 0.8055 (pp20) cc_final: 0.7529 (pp20) REVERT: 1 27 MET cc_start: 0.7474 (mmm) cc_final: 0.7202 (mmm) REVERT: 2 12 CYS cc_start: 0.6022 (t) cc_final: 0.5622 (t) REVERT: 2 14 GLU cc_start: 0.8150 (pm20) cc_final: 0.7654 (pm20) REVERT: 3 1 MET cc_start: 0.4985 (mmm) cc_final: 0.4578 (mmp) REVERT: 3 11 LYS cc_start: 0.8439 (mttt) cc_final: 0.8200 (mttp) REVERT: 4 23 LYS cc_start: 0.7209 (tmmt) cc_final: 0.6742 (pttp) REVERT: 4 35 ASN cc_start: 0.8519 (m-40) cc_final: 0.8120 (m-40) REVERT: 4 56 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8394 (ttmm) REVERT: 5 1 MET cc_start: 0.8961 (tpp) cc_final: 0.8551 (tpp) REVERT: 5 4 ARG cc_start: 0.8164 (ptp-170) cc_final: 0.7888 (ptm160) REVERT: Z 10 LYS cc_start: 0.7513 (pttm) cc_final: 0.6749 (mtmm) REVERT: Z 28 LYS cc_start: 0.7312 (tmmt) cc_final: 0.7086 (tmmt) REVERT: b 27 MET cc_start: 0.7758 (mpp) cc_final: 0.7396 (mmm) REVERT: b 45 LYS cc_start: 0.9502 (mtmt) cc_final: 0.9199 (mtmt) REVERT: b 142 GLU cc_start: 0.7682 (pp20) cc_final: 0.7239 (pp20) REVERT: b 178 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7960 (tptp) REVERT: c 31 PHE cc_start: 0.8575 (m-80) cc_final: 0.8015 (m-80) REVERT: c 101 ASN cc_start: 0.8256 (t0) cc_final: 0.8046 (t0) REVERT: d 47 TYR cc_start: 0.8549 (t80) cc_final: 0.8105 (t80) REVERT: d 50 GLN cc_start: 0.9355 (mt0) cc_final: 0.8535 (mm-40) REVERT: d 59 HIS cc_start: 0.8221 (m-70) cc_final: 0.7577 (m-70) REVERT: d 196 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7048 (mt-10) REVERT: d 198 TYR cc_start: 0.8164 (m-80) cc_final: 0.7764 (m-10) REVERT: e 76 MET cc_start: 0.7045 (mmt) cc_final: 0.6564 (mmm) REVERT: e 88 ARG cc_start: 0.7465 (mtt-85) cc_final: 0.6943 (mmt180) REVERT: e 93 ASN cc_start: 0.8123 (m-40) cc_final: 0.5897 (t0) REVERT: e 141 LEU cc_start: 0.9278 (mm) cc_final: 0.8565 (tt) REVERT: e 147 LEU cc_start: 0.9007 (mt) cc_final: 0.8591 (mt) REVERT: e 152 ASP cc_start: 0.8977 (m-30) cc_final: 0.8702 (m-30) REVERT: f 5 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7369 (tm-30) REVERT: f 8 TYR cc_start: 0.8943 (p90) cc_final: 0.8653 (p90) REVERT: f 19 LYS cc_start: 0.8881 (mtmm) cc_final: 0.7968 (mttm) REVERT: f 46 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.8020 (ttm-80) REVERT: f 62 ILE cc_start: 0.8183 (mp) cc_final: 0.7275 (mp) REVERT: g 11 ASP cc_start: 0.7784 (p0) cc_final: 0.7253 (p0) REVERT: g 17 ILE cc_start: 0.8810 (pt) cc_final: 0.7856 (pt) REVERT: g 28 ASN cc_start: 0.8933 (m-40) cc_final: 0.8638 (m-40) REVERT: g 31 MET cc_start: 0.8984 (ttm) cc_final: 0.8505 (ttp) REVERT: g 57 ASP cc_start: 0.8071 (m-30) cc_final: 0.7810 (t70) REVERT: g 59 MET cc_start: 0.8893 (mmm) cc_final: 0.8590 (mmm) REVERT: g 61 VAL cc_start: 0.9243 (t) cc_final: 0.9016 (t) REVERT: g 68 ASN cc_start: 0.9314 (m-40) cc_final: 0.8888 (m-40) REVERT: g 122 ASN cc_start: 0.8763 (m-40) cc_final: 0.8419 (m110) REVERT: g 130 ASN cc_start: 0.8611 (p0) cc_final: 0.8018 (p0) REVERT: h 35 GLU cc_start: 0.9011 (mp0) cc_final: 0.8663 (mp0) REVERT: h 39 ILE cc_start: 0.8935 (mm) cc_final: 0.8168 (mm) REVERT: h 66 TYR cc_start: 0.8119 (m-10) cc_final: 0.7885 (m-80) REVERT: h 98 LEU cc_start: 0.9157 (mt) cc_final: 0.8597 (mm) REVERT: h 101 LEU cc_start: 0.9108 (tt) cc_final: 0.8894 (tt) REVERT: h 126 GLU cc_start: 0.8281 (tp30) cc_final: 0.8013 (tp30) REVERT: h 127 VAL cc_start: 0.8914 (t) cc_final: 0.8441 (t) REVERT: i 13 LYS cc_start: 0.9085 (ttmt) cc_final: 0.8782 (ttmt) REVERT: i 34 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7463 (mm-30) REVERT: i 46 GLU cc_start: 0.7935 (pt0) cc_final: 0.7734 (pt0) REVERT: i 49 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8724 (mtmm) REVERT: j 10 LEU cc_start: 0.9007 (mm) cc_final: 0.8758 (mm) REVERT: j 61 SER cc_start: 0.9121 (p) cc_final: 0.8850 (p) REVERT: j 63 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8025 (mt-10) REVERT: j 90 LEU cc_start: 0.9240 (mt) cc_final: 0.8945 (mt) REVERT: k 54 PHE cc_start: 0.7925 (m-80) cc_final: 0.7656 (m-80) REVERT: k 63 PHE cc_start: 0.8509 (t80) cc_final: 0.7771 (t80) REVERT: k 66 GLN cc_start: 0.9027 (pp30) cc_final: 0.7985 (pp30) REVERT: k 83 THR cc_start: 0.9235 (p) cc_final: 0.8859 (p) REVERT: k 88 VAL cc_start: 0.9429 (t) cc_final: 0.9100 (m) REVERT: l 35 HIS cc_start: 0.7814 (m-70) cc_final: 0.7184 (m90) REVERT: l 128 SER cc_start: 0.8735 (p) cc_final: 0.8523 (p) REVERT: m 76 ASN cc_start: 0.8618 (m110) cc_final: 0.8380 (m-40) REVERT: m 87 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8345 (ttt90) REVERT: m 100 GLN cc_start: 0.8918 (mp10) cc_final: 0.8598 (mp10) REVERT: n 6 MET cc_start: 0.8533 (tpp) cc_final: 0.7924 (tpp) REVERT: n 7 ILE cc_start: 0.8916 (mt) cc_final: 0.8467 (mt) REVERT: n 21 TYR cc_start: 0.8620 (p90) cc_final: 0.7721 (p90) REVERT: n 39 LEU cc_start: 0.9227 (mt) cc_final: 0.8466 (tp) REVERT: n 47 LEU cc_start: 0.9325 (mt) cc_final: 0.8969 (mt) REVERT: o 7 ARG cc_start: 0.8723 (tpt90) cc_final: 0.7878 (tpt90) REVERT: o 11 LEU cc_start: 0.9248 (mt) cc_final: 0.8723 (mt) REVERT: o 54 ARG cc_start: 0.8567 (ttt90) cc_final: 0.8300 (tpt170) REVERT: o 62 LYS cc_start: 0.8778 (mttt) cc_final: 0.8577 (mmmt) REVERT: p 6 ARG cc_start: 0.9019 (ptt180) cc_final: 0.8371 (ptt90) REVERT: p 25 SER cc_start: 0.9265 (p) cc_final: 0.8938 (p) REVERT: p 65 LYS cc_start: 0.8842 (mttt) cc_final: 0.8527 (mttm) REVERT: p 71 ARG cc_start: 0.8426 (tpt90) cc_final: 0.7932 (tpt90) REVERT: p 79 ILE cc_start: 0.8879 (mp) cc_final: 0.8509 (mp) REVERT: q 19 MET cc_start: 0.7604 (mpp) cc_final: 0.7234 (mmp) REVERT: q 41 LYS cc_start: 0.8789 (pttt) cc_final: 0.8113 (ptpp) REVERT: q 56 LYS cc_start: 0.8078 (mttt) cc_final: 0.7787 (mmtt) REVERT: r 33 LEU cc_start: 0.9490 (mt) cc_final: 0.8916 (mt) REVERT: r 36 LYS cc_start: 0.9335 (mtmm) cc_final: 0.8961 (mttp) REVERT: r 43 LYS cc_start: 0.8388 (mtmm) cc_final: 0.7945 (mttp) REVERT: r 45 LEU cc_start: 0.9001 (mt) cc_final: 0.8527 (mt) REVERT: r 48 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7618 (mtt180) REVERT: r 75 TYR cc_start: 0.8231 (m-80) cc_final: 0.7465 (m-10) REVERT: t 49 THR cc_start: 0.9537 (p) cc_final: 0.8952 (p) REVERT: t 60 LYS cc_start: 0.8828 (mttt) cc_final: 0.8017 (ttmm) REVERT: t 86 LEU cc_start: 0.8754 (pp) cc_final: 0.8538 (pp) REVERT: x 395 TYR cc_start: 0.7404 (m-80) cc_final: 0.7156 (m-10) REVERT: x 464 TRP cc_start: 0.8299 (m-90) cc_final: 0.7785 (m-10) REVERT: x 533 TYR cc_start: 0.5693 (m-80) cc_final: 0.5475 (m-80) REVERT: x 658 ASN cc_start: 0.8615 (m-40) cc_final: 0.8225 (m110) REVERT: x 700 THR cc_start: 0.8968 (p) cc_final: 0.8343 (p) outliers start: 4 outliers final: 1 residues processed: 1964 average time/residue: 1.2803 time to fit residues: 4322.7626 Evaluate side-chains 1679 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1678 time to evaluate : 5.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 605 optimal weight: 30.0000 chunk 391 optimal weight: 20.0000 chunk 584 optimal weight: 40.0000 chunk 294 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 622 optimal weight: 10.0000 chunk 667 optimal weight: 10.0000 chunk 484 optimal weight: 7.9990 chunk 91 optimal weight: 30.0000 chunk 769 optimal weight: 0.7980 overall best weight: 7.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 62 ASN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN ** J 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 HIS K 4 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS U 58 ASN ** W 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 HIS ** 1 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 4 ASN ** 2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 122 GLN d 52 GLN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 ASN ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS t 68 HIS t 70 ASN ** x 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 159537 Z= 0.390 Angle : 0.818 15.462 238979 Z= 0.408 Chirality : 0.043 0.386 30585 Planarity : 0.007 0.120 12519 Dihedral : 25.290 179.941 80645 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 27.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.35 % Favored : 87.52 % Rotamer: Outliers : 0.02 % Allowed : 2.02 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.96 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.11), residues: 5546 helix: -1.08 (0.12), residues: 1651 sheet: -1.27 (0.18), residues: 842 loop : -2.47 (0.10), residues: 3053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP b 96 HIS 0.017 0.002 HIS C 53 PHE 0.030 0.003 PHE s 10 TYR 0.053 0.003 TYR c 28 ARG 0.032 0.001 ARG b 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1964 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1963 time to evaluate : 8.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ILE cc_start: 0.8454 (mt) cc_final: 0.8148 (mt) REVERT: C 32 SER cc_start: 0.8709 (p) cc_final: 0.8229 (m) REVERT: C 115 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7408 (tm-30) REVERT: C 116 ILE cc_start: 0.8893 (mt) cc_final: 0.8629 (mt) REVERT: C 198 GLU cc_start: 0.8027 (tt0) cc_final: 0.7634 (tp30) REVERT: D 100 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7591 (tm-30) REVERT: D 169 ILE cc_start: 0.8117 (mt) cc_final: 0.7833 (mt) REVERT: D 185 LEU cc_start: 0.9163 (mt) cc_final: 0.8791 (mp) REVERT: D 186 LEU cc_start: 0.9190 (mt) cc_final: 0.8723 (mt) REVERT: D 198 SER cc_start: 0.8386 (m) cc_final: 0.8076 (p) REVERT: E 40 GLN cc_start: 0.8886 (tt0) cc_final: 0.8460 (tt0) REVERT: E 161 GLU cc_start: 0.8535 (pp20) cc_final: 0.8206 (pp20) REVERT: E 165 LEU cc_start: 0.9280 (mt) cc_final: 0.9047 (tt) REVERT: E 184 LEU cc_start: 0.9269 (pp) cc_final: 0.8705 (pp) REVERT: E 185 ASP cc_start: 0.8812 (m-30) cc_final: 0.8526 (m-30) REVERT: E 200 GLU cc_start: 0.9149 (mp0) cc_final: 0.8944 (mp0) REVERT: F 78 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7265 (ttm110) REVERT: F 81 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8063 (mm-30) REVERT: F 138 PHE cc_start: 0.7358 (p90) cc_final: 0.6861 (p90) REVERT: F 170 LEU cc_start: 0.8959 (mt) cc_final: 0.8650 (mt) REVERT: G 75 ASN cc_start: 0.8898 (m110) cc_final: 0.8524 (t0) REVERT: G 84 PHE cc_start: 0.8687 (m-80) cc_final: 0.8329 (m-80) REVERT: G 172 ARG cc_start: 0.8680 (mmp80) cc_final: 0.8162 (mmm160) REVERT: J 109 MET cc_start: 0.8646 (mtp) cc_final: 0.8256 (mtp) REVERT: J 119 MET cc_start: 0.8418 (mtm) cc_final: 0.8172 (mtp) REVERT: K 2 ILE cc_start: 0.8501 (mt) cc_final: 0.8063 (mm) REVERT: K 54 LYS cc_start: 0.7990 (tttp) cc_final: 0.7569 (ttpt) REVERT: L 23 ILE cc_start: 0.7522 (pt) cc_final: 0.7087 (tp) REVERT: M 25 THR cc_start: 0.8969 (p) cc_final: 0.8276 (p) REVERT: M 32 PHE cc_start: 0.7870 (m-10) cc_final: 0.7651 (m-10) REVERT: M 44 ASN cc_start: 0.8639 (p0) cc_final: 0.8298 (p0) REVERT: M 59 LYS cc_start: 0.9203 (tmtt) cc_final: 0.8907 (tptp) REVERT: M 124 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8926 (mmmt) REVERT: M 128 LYS cc_start: 0.8962 (tttt) cc_final: 0.8270 (tttp) REVERT: N 56 LEU cc_start: 0.8956 (tp) cc_final: 0.8756 (tp) REVERT: N 59 ARG cc_start: 0.8296 (tpp80) cc_final: 0.7722 (tpp80) REVERT: N 77 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8762 (tp-100) REVERT: N 81 GLN cc_start: 0.8435 (mt0) cc_final: 0.8043 (mt0) REVERT: N 82 LYS cc_start: 0.8782 (tttm) cc_final: 0.8169 (tttt) REVERT: N 83 LEU cc_start: 0.9460 (tp) cc_final: 0.9190 (tp) REVERT: N 95 GLN cc_start: 0.8458 (mt0) cc_final: 0.8015 (mp10) REVERT: N 118 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6711 (tm-30) REVERT: O 38 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8690 (mmtp) REVERT: O 118 LEU cc_start: 0.9170 (mm) cc_final: 0.8885 (mm) REVERT: P 13 LEU cc_start: 0.9014 (mt) cc_final: 0.8738 (mp) REVERT: Q 32 TYR cc_start: 0.8877 (t80) cc_final: 0.8380 (t80) REVERT: Q 37 GLN cc_start: 0.7301 (mt0) cc_final: 0.6112 (tm-30) REVERT: Q 45 TYR cc_start: 0.8761 (m-10) cc_final: 0.8029 (m-10) REVERT: Q 59 LYS cc_start: 0.7859 (ttmt) cc_final: 0.7601 (ttmt) REVERT: Q 61 TRP cc_start: 0.9147 (m-10) cc_final: 0.8900 (m-10) REVERT: R 69 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8414 (tppt) REVERT: S 37 ASN cc_start: 0.7834 (m110) cc_final: 0.7585 (m110) REVERT: S 62 TYR cc_start: 0.7071 (m-80) cc_final: 0.6780 (m-80) REVERT: S 65 ASP cc_start: 0.8658 (t0) cc_final: 0.8233 (t70) REVERT: S 68 ASN cc_start: 0.7632 (p0) cc_final: 0.7041 (p0) REVERT: T 3 ASP cc_start: 0.8695 (p0) cc_final: 0.8435 (p0) REVERT: T 13 ILE cc_start: 0.9141 (mp) cc_final: 0.8686 (tp) REVERT: T 21 MET cc_start: 0.8853 (mtm) cc_final: 0.7989 (mtt) REVERT: T 22 THR cc_start: 0.9611 (p) cc_final: 0.9313 (p) REVERT: T 28 PHE cc_start: 0.8034 (m-80) cc_final: 0.7770 (m-80) REVERT: T 57 MET cc_start: 0.7236 (mtp) cc_final: 0.6918 (mtp) REVERT: U 64 HIS cc_start: 0.8629 (t-90) cc_final: 0.7779 (t-170) REVERT: U 99 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8540 (mm-40) REVERT: V 22 ARG cc_start: 0.7556 (pmt170) cc_final: 0.7122 (ptt-90) REVERT: V 46 TYR cc_start: 0.7807 (t80) cc_final: 0.7582 (t80) REVERT: V 68 PHE cc_start: 0.8264 (p90) cc_final: 0.8053 (p90) REVERT: X 24 GLU cc_start: 0.8672 (pt0) cc_final: 0.8406 (pt0) REVERT: X 28 LEU cc_start: 0.9125 (mm) cc_final: 0.8871 (tp) REVERT: X 52 ARG cc_start: 0.8781 (ptm160) cc_final: 0.8498 (ptm-80) REVERT: Y 30 LYS cc_start: 0.8834 (mttt) cc_final: 0.8386 (mmmt) REVERT: Y 38 GLU cc_start: 0.8044 (pp20) cc_final: 0.7545 (pp20) REVERT: 1 21 LYS cc_start: 0.7267 (pttt) cc_final: 0.6273 (mmtm) REVERT: 1 27 MET cc_start: 0.7409 (mmm) cc_final: 0.7183 (mmm) REVERT: 2 12 CYS cc_start: 0.6267 (t) cc_final: 0.5839 (t) REVERT: 2 14 GLU cc_start: 0.8260 (pm20) cc_final: 0.7698 (pm20) REVERT: 3 1 MET cc_start: 0.5085 (mmm) cc_final: 0.4737 (mmp) REVERT: 3 11 LYS cc_start: 0.8454 (mttt) cc_final: 0.8219 (mttp) REVERT: 4 23 LYS cc_start: 0.7264 (tmmt) cc_final: 0.6909 (pttp) REVERT: 4 35 ASN cc_start: 0.8439 (m-40) cc_final: 0.8049 (m-40) REVERT: 4 56 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8594 (ttmm) REVERT: 4 59 LYS cc_start: 0.8349 (ptpt) cc_final: 0.7911 (pttt) REVERT: 5 1 MET cc_start: 0.8902 (tpp) cc_final: 0.8565 (tpp) REVERT: 5 4 ARG cc_start: 0.8205 (ptp-170) cc_final: 0.7924 (ptm160) REVERT: Z 28 LYS cc_start: 0.7356 (tmmt) cc_final: 0.7068 (tmmt) REVERT: b 27 MET cc_start: 0.7683 (mpp) cc_final: 0.7471 (mmt) REVERT: b 45 LYS cc_start: 0.9511 (mtmt) cc_final: 0.9223 (mtmt) REVERT: b 135 VAL cc_start: 0.7436 (t) cc_final: 0.7194 (t) REVERT: b 178 LYS cc_start: 0.8516 (ttmt) cc_final: 0.7904 (tptm) REVERT: c 31 PHE cc_start: 0.8429 (m-80) cc_final: 0.7858 (m-80) REVERT: c 33 HIS cc_start: 0.8671 (m90) cc_final: 0.7536 (m90) REVERT: c 101 ASN cc_start: 0.8350 (t0) cc_final: 0.8108 (t0) REVERT: c 182 ASP cc_start: 0.8033 (t70) cc_final: 0.7590 (t0) REVERT: d 47 TYR cc_start: 0.8586 (t80) cc_final: 0.8074 (t80) REVERT: d 50 GLN cc_start: 0.9317 (mt0) cc_final: 0.8458 (mm-40) REVERT: d 59 HIS cc_start: 0.8216 (m-70) cc_final: 0.7557 (m-70) REVERT: d 71 LEU cc_start: 0.8750 (mt) cc_final: 0.8425 (mt) REVERT: d 87 MET cc_start: 0.8560 (mtm) cc_final: 0.7926 (mtp) REVERT: d 196 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7147 (mt-10) REVERT: d 198 TYR cc_start: 0.8179 (m-80) cc_final: 0.7645 (m-10) REVERT: e 88 ARG cc_start: 0.7416 (mtt-85) cc_final: 0.6955 (mmt180) REVERT: e 93 ASN cc_start: 0.8121 (m-40) cc_final: 0.6646 (m-40) REVERT: e 95 LEU cc_start: 0.8178 (pt) cc_final: 0.7896 (pt) REVERT: e 141 LEU cc_start: 0.9264 (mm) cc_final: 0.8600 (tt) REVERT: e 144 LEU cc_start: 0.9188 (mt) cc_final: 0.8976 (mt) REVERT: e 147 LEU cc_start: 0.9072 (mt) cc_final: 0.8742 (mt) REVERT: e 152 ASP cc_start: 0.8847 (m-30) cc_final: 0.8521 (m-30) REVERT: f 5 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7688 (tm-30) REVERT: f 8 TYR cc_start: 0.9082 (p90) cc_final: 0.8818 (p90) REVERT: f 19 LYS cc_start: 0.8842 (mtmm) cc_final: 0.7899 (mttm) REVERT: f 27 ASN cc_start: 0.9368 (m-40) cc_final: 0.9157 (m-40) REVERT: f 51 GLU cc_start: 0.8526 (tp30) cc_final: 0.8243 (tm-30) REVERT: f 61 GLN cc_start: 0.7961 (mp10) cc_final: 0.7357 (mp10) REVERT: g 17 ILE cc_start: 0.8825 (pt) cc_final: 0.7851 (pt) REVERT: g 28 ASN cc_start: 0.8926 (m-40) cc_final: 0.8690 (m-40) REVERT: g 31 MET cc_start: 0.8956 (ttm) cc_final: 0.8463 (ttp) REVERT: g 57 ASP cc_start: 0.7975 (m-30) cc_final: 0.7749 (t70) REVERT: g 61 VAL cc_start: 0.9285 (t) cc_final: 0.9082 (t) REVERT: g 68 ASN cc_start: 0.9371 (m-40) cc_final: 0.8959 (m-40) REVERT: g 116 MET cc_start: 0.8039 (tpp) cc_final: 0.7824 (tpp) REVERT: g 122 ASN cc_start: 0.8789 (m-40) cc_final: 0.8436 (m110) REVERT: g 130 ASN cc_start: 0.8717 (p0) cc_final: 0.8131 (p0) REVERT: h 35 GLU cc_start: 0.9015 (mp0) cc_final: 0.8692 (mp0) REVERT: h 39 ILE cc_start: 0.9084 (mm) cc_final: 0.8280 (mm) REVERT: h 40 LEU cc_start: 0.9549 (mm) cc_final: 0.9273 (mm) REVERT: h 46 ILE cc_start: 0.8975 (mm) cc_final: 0.8632 (mm) REVERT: h 66 TYR cc_start: 0.8227 (m-10) cc_final: 0.7863 (m-80) REVERT: h 98 LEU cc_start: 0.9169 (mt) cc_final: 0.8589 (mm) REVERT: h 101 LEU cc_start: 0.9194 (tt) cc_final: 0.8978 (tt) REVERT: h 127 VAL cc_start: 0.8844 (t) cc_final: 0.8600 (t) REVERT: i 13 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8903 (ttmt) REVERT: i 34 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7484 (mm-30) REVERT: j 10 LEU cc_start: 0.9037 (mm) cc_final: 0.8798 (mm) REVERT: j 63 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8232 (mt-10) REVERT: j 90 LEU cc_start: 0.9271 (mt) cc_final: 0.8948 (mt) REVERT: j 92 LEU cc_start: 0.8784 (mm) cc_final: 0.8324 (mm) REVERT: k 54 PHE cc_start: 0.8145 (m-80) cc_final: 0.7582 (m-10) REVERT: k 67 MET cc_start: 0.8282 (mpp) cc_final: 0.8015 (mpp) REVERT: k 83 THR cc_start: 0.9208 (p) cc_final: 0.8877 (p) REVERT: k 88 VAL cc_start: 0.9435 (t) cc_final: 0.9137 (m) REVERT: k 128 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7979 (mtp180) REVERT: l 24 LEU cc_start: 0.9270 (mt) cc_final: 0.9070 (mt) REVERT: l 34 GLU cc_start: 0.8197 (pp20) cc_final: 0.7981 (pp20) REVERT: l 35 HIS cc_start: 0.7877 (m-70) cc_final: 0.7239 (m90) REVERT: l 128 SER cc_start: 0.8733 (p) cc_final: 0.8517 (p) REVERT: m 31 GLN cc_start: 0.9341 (mt0) cc_final: 0.8797 (mt0) REVERT: m 76 ASN cc_start: 0.8731 (m110) cc_final: 0.8503 (m-40) REVERT: m 87 ARG cc_start: 0.9014 (ttp80) cc_final: 0.8458 (ttt90) REVERT: m 100 GLN cc_start: 0.8916 (mp10) cc_final: 0.8613 (mp10) REVERT: n 6 MET cc_start: 0.8672 (tpp) cc_final: 0.8084 (tpp) REVERT: n 9 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8364 (tttt) REVERT: n 17 LYS cc_start: 0.8477 (tptp) cc_final: 0.7989 (tptt) REVERT: n 21 TYR cc_start: 0.8679 (p90) cc_final: 0.7929 (p90) REVERT: n 39 LEU cc_start: 0.9184 (mt) cc_final: 0.8494 (tp) REVERT: o 7 ARG cc_start: 0.8705 (tpt90) cc_final: 0.8040 (tpt90) REVERT: o 11 LEU cc_start: 0.9254 (mt) cc_final: 0.8894 (mt) REVERT: p 6 ARG cc_start: 0.9113 (ptt180) cc_final: 0.8448 (ptt90) REVERT: p 19 ARG cc_start: 0.9086 (ttm170) cc_final: 0.8810 (ttm170) REVERT: p 65 LYS cc_start: 0.8833 (mttt) cc_final: 0.8417 (mttm) REVERT: p 79 ILE cc_start: 0.8770 (mp) cc_final: 0.8216 (mp) REVERT: p 83 PHE cc_start: 0.8860 (t80) cc_final: 0.8549 (t80) REVERT: q 19 MET cc_start: 0.7538 (mpp) cc_final: 0.7206 (mmp) REVERT: q 41 LYS cc_start: 0.8755 (pttt) cc_final: 0.8253 (ptpt) REVERT: q 56 LYS cc_start: 0.8052 (mttt) cc_final: 0.7758 (mmtt) REVERT: r 33 LEU cc_start: 0.9490 (mt) cc_final: 0.8806 (mt) REVERT: r 35 LYS cc_start: 0.9264 (mtmm) cc_final: 0.8936 (mtmm) REVERT: r 36 LYS cc_start: 0.9308 (mtmm) cc_final: 0.8963 (mttp) REVERT: r 43 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7976 (mttp) REVERT: r 45 LEU cc_start: 0.9055 (mt) cc_final: 0.8598 (mt) REVERT: r 48 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7717 (mtt180) REVERT: r 66 ARG cc_start: 0.9300 (ptp-170) cc_final: 0.8969 (ptp-170) REVERT: r 75 TYR cc_start: 0.8311 (m-80) cc_final: 0.7524 (m-80) REVERT: t 49 THR cc_start: 0.9586 (p) cc_final: 0.9312 (p) REVERT: t 60 LYS cc_start: 0.8885 (mttt) cc_final: 0.8049 (ttmm) REVERT: t 71 THR cc_start: 0.8600 (m) cc_final: 0.8232 (m) REVERT: x 464 TRP cc_start: 0.8355 (m-90) cc_final: 0.7843 (m-10) REVERT: x 595 LEU cc_start: 0.9364 (mt) cc_final: 0.9110 (mt) REVERT: x 658 ASN cc_start: 0.8646 (m-40) cc_final: 0.8287 (m-40) REVERT: x 700 THR cc_start: 0.8996 (p) cc_final: 0.8404 (p) REVERT: x 731 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8062 (ttp80) outliers start: 1 outliers final: 0 residues processed: 1963 average time/residue: 1.3004 time to fit residues: 4385.7613 Evaluate side-chains 1660 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1660 time to evaluate : 6.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 890 optimal weight: 6.9990 chunk 938 optimal weight: 30.0000 chunk 855 optimal weight: 9.9990 chunk 912 optimal weight: 7.9990 chunk 937 optimal weight: 20.0000 chunk 549 optimal weight: 9.9990 chunk 397 optimal weight: 7.9990 chunk 716 optimal weight: 20.0000 chunk 280 optimal weight: 9.9990 chunk 824 optimal weight: 0.8980 chunk 863 optimal weight: 0.0370 overall best weight: 4.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 62 ASN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 ASN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 GLN U 58 ASN ** W 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 4 ASN ** 2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 26 ASN ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 122 GLN c 135 GLN d 52 GLN ** d 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 ASN ** k 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 121 ASN ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 ASN m 32 GLN ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS ** t 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 159537 Z= 0.265 Angle : 0.710 15.042 238979 Z= 0.361 Chirality : 0.039 0.387 30585 Planarity : 0.006 0.102 12519 Dihedral : 25.228 179.971 80645 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.94 % Favored : 88.93 % Rotamer: Outliers : 0.04 % Allowed : 0.74 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.96 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.11), residues: 5546 helix: -1.00 (0.12), residues: 1658 sheet: -1.20 (0.18), residues: 878 loop : -2.41 (0.10), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP b 96 HIS 0.011 0.002 HIS f 88 PHE 0.034 0.003 PHE b 69 TYR 0.028 0.002 TYR c 28 ARG 0.016 0.001 ARG p 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1977 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1975 time to evaluate : 6.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 SER cc_start: 0.8626 (p) cc_final: 0.8147 (m) REVERT: C 115 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7480 (tm-30) REVERT: C 116 ILE cc_start: 0.8886 (mt) cc_final: 0.8656 (mt) REVERT: C 198 GLU cc_start: 0.7923 (tt0) cc_final: 0.7520 (tp30) REVERT: D 100 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7582 (tm-30) REVERT: D 173 ASN cc_start: 0.7115 (t0) cc_final: 0.6481 (t0) REVERT: D 185 LEU cc_start: 0.9136 (mt) cc_final: 0.8783 (mp) REVERT: D 186 LEU cc_start: 0.9160 (mt) cc_final: 0.8727 (mt) REVERT: E 40 GLN cc_start: 0.8764 (tt0) cc_final: 0.8290 (tt0) REVERT: E 184 LEU cc_start: 0.9271 (pp) cc_final: 0.8750 (pp) REVERT: E 185 ASP cc_start: 0.8808 (m-30) cc_final: 0.8512 (m-30) REVERT: E 200 GLU cc_start: 0.9085 (mp0) cc_final: 0.8884 (mp0) REVERT: F 81 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7955 (mm-30) REVERT: F 138 PHE cc_start: 0.7115 (p90) cc_final: 0.6653 (p90) REVERT: F 154 ILE cc_start: 0.8350 (mm) cc_final: 0.8109 (mm) REVERT: F 170 LEU cc_start: 0.8896 (mt) cc_final: 0.8443 (mt) REVERT: G 75 ASN cc_start: 0.8923 (m110) cc_final: 0.8540 (t0) REVERT: G 84 PHE cc_start: 0.8659 (m-80) cc_final: 0.8219 (m-80) REVERT: J 50 ASP cc_start: 0.8192 (t70) cc_final: 0.6225 (t70) REVERT: J 109 MET cc_start: 0.8544 (mtp) cc_final: 0.8256 (mtp) REVERT: J 119 MET cc_start: 0.8338 (mtm) cc_final: 0.7761 (mmm) REVERT: K 2 ILE cc_start: 0.8517 (mt) cc_final: 0.8121 (mm) REVERT: K 5 GLU cc_start: 0.8677 (mp0) cc_final: 0.8019 (mp0) REVERT: K 54 LYS cc_start: 0.8017 (tttp) cc_final: 0.7682 (ttpt) REVERT: L 23 ILE cc_start: 0.7471 (pt) cc_final: 0.7053 (tp) REVERT: M 25 THR cc_start: 0.8873 (p) cc_final: 0.8576 (p) REVERT: M 32 PHE cc_start: 0.7795 (m-10) cc_final: 0.7495 (m-10) REVERT: M 44 ASN cc_start: 0.8668 (p0) cc_final: 0.8361 (p0) REVERT: M 57 TYR cc_start: 0.8507 (t80) cc_final: 0.8145 (t80) REVERT: M 59 LYS cc_start: 0.9258 (tmtt) cc_final: 0.8986 (tptp) REVERT: M 74 TYR cc_start: 0.8026 (p90) cc_final: 0.7716 (p90) REVERT: M 113 VAL cc_start: 0.9269 (t) cc_final: 0.9061 (t) REVERT: M 128 LYS cc_start: 0.8853 (tttt) cc_final: 0.8224 (tttt) REVERT: N 56 LEU cc_start: 0.8954 (tp) cc_final: 0.8751 (tp) REVERT: N 59 ARG cc_start: 0.8367 (tpp80) cc_final: 0.7815 (tpp80) REVERT: N 81 GLN cc_start: 0.8345 (mt0) cc_final: 0.8005 (mt0) REVERT: N 82 LYS cc_start: 0.8789 (tttm) cc_final: 0.8228 (tttt) REVERT: N 95 GLN cc_start: 0.8375 (mt0) cc_final: 0.7971 (mp10) REVERT: N 116 ILE cc_start: 0.8519 (mt) cc_final: 0.8228 (mt) REVERT: N 118 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6712 (tm-30) REVERT: O 38 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8505 (mmtt) REVERT: O 39 HIS cc_start: 0.7314 (m-70) cc_final: 0.5740 (m-70) REVERT: O 58 THR cc_start: 0.8343 (p) cc_final: 0.7848 (p) REVERT: O 118 LEU cc_start: 0.9183 (mm) cc_final: 0.8906 (mm) REVERT: P 48 ILE cc_start: 0.8724 (mt) cc_final: 0.8462 (pt) REVERT: Q 37 GLN cc_start: 0.7380 (mt0) cc_final: 0.6076 (tm-30) REVERT: Q 45 TYR cc_start: 0.8574 (m-10) cc_final: 0.7989 (m-10) REVERT: Q 59 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7552 (ttpp) REVERT: Q 61 TRP cc_start: 0.9136 (m-10) cc_final: 0.8874 (m-10) REVERT: R 69 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8337 (tppt) REVERT: S 48 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8259 (mt-10) REVERT: S 106 VAL cc_start: 0.8434 (t) cc_final: 0.7522 (t) REVERT: T 13 ILE cc_start: 0.9210 (mp) cc_final: 0.8704 (tp) REVERT: T 21 MET cc_start: 0.8834 (mtm) cc_final: 0.8142 (mtt) REVERT: T 28 PHE cc_start: 0.8030 (m-80) cc_final: 0.7720 (m-80) REVERT: T 37 THR cc_start: 0.8784 (p) cc_final: 0.8571 (p) REVERT: T 57 MET cc_start: 0.7057 (mtp) cc_final: 0.6748 (mtp) REVERT: U 1 MET cc_start: 0.7346 (mtt) cc_final: 0.6207 (mpp) REVERT: U 9 VAL cc_start: 0.9144 (t) cc_final: 0.8833 (p) REVERT: U 64 HIS cc_start: 0.8555 (t-90) cc_final: 0.7820 (t-170) REVERT: U 99 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8510 (mm-40) REVERT: V 19 LYS cc_start: 0.8830 (tppt) cc_final: 0.8439 (tptp) REVERT: V 22 ARG cc_start: 0.7580 (pmt170) cc_final: 0.7065 (ptt-90) REVERT: V 46 TYR cc_start: 0.7727 (t80) cc_final: 0.7455 (t80) REVERT: X 24 GLU cc_start: 0.8648 (pt0) cc_final: 0.8395 (pt0) REVERT: X 28 LEU cc_start: 0.9168 (mm) cc_final: 0.8890 (tp) REVERT: X 43 ILE cc_start: 0.9290 (mp) cc_final: 0.9061 (mp) REVERT: Y 30 LYS cc_start: 0.8796 (mttt) cc_final: 0.8388 (mmmt) REVERT: Y 38 GLU cc_start: 0.8027 (pp20) cc_final: 0.7560 (pp20) REVERT: 1 38 LEU cc_start: 0.8702 (tp) cc_final: 0.8434 (tp) REVERT: 2 10 THR cc_start: 0.8453 (p) cc_final: 0.8156 (p) REVERT: 2 12 CYS cc_start: 0.5984 (t) cc_final: 0.5711 (t) REVERT: 2 44 LEU cc_start: 0.8862 (tp) cc_final: 0.8470 (tt) REVERT: 3 1 MET cc_start: 0.4963 (mmm) cc_final: 0.4559 (mmp) REVERT: 4 23 LYS cc_start: 0.7171 (tmmt) cc_final: 0.6735 (pttp) REVERT: 4 56 LYS cc_start: 0.8823 (ttpp) cc_final: 0.7907 (ttmm) REVERT: 5 1 MET cc_start: 0.8898 (tpp) cc_final: 0.8508 (tpp) REVERT: 5 18 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7946 (tpp80) REVERT: 5 34 GLN cc_start: 0.8288 (mt0) cc_final: 0.7943 (tt0) REVERT: b 27 MET cc_start: 0.7859 (mpp) cc_final: 0.7587 (mpp) REVERT: b 45 LYS cc_start: 0.9470 (mtmt) cc_final: 0.9169 (mtmt) REVERT: b 100 THR cc_start: 0.8889 (p) cc_final: 0.8647 (p) REVERT: b 103 ASN cc_start: 0.7830 (t0) cc_final: 0.7627 (t0) REVERT: b 141 LEU cc_start: 0.9321 (mt) cc_final: 0.8877 (mt) REVERT: b 177 ARG cc_start: 0.8833 (ttt90) cc_final: 0.8486 (ttm170) REVERT: b 178 LYS cc_start: 0.8505 (ttmt) cc_final: 0.7956 (tptp) REVERT: c 31 PHE cc_start: 0.8505 (m-80) cc_final: 0.7852 (m-80) REVERT: c 33 HIS cc_start: 0.8677 (m90) cc_final: 0.7443 (m90) REVERT: c 88 LYS cc_start: 0.9274 (ptpp) cc_final: 0.8897 (ptpp) REVERT: c 101 ASN cc_start: 0.8205 (t0) cc_final: 0.7996 (t0) REVERT: c 182 ASP cc_start: 0.7815 (t70) cc_final: 0.7546 (t0) REVERT: d 47 TYR cc_start: 0.8610 (t80) cc_final: 0.8191 (t80) REVERT: d 50 GLN cc_start: 0.9278 (mt0) cc_final: 0.8402 (mm-40) REVERT: d 59 HIS cc_start: 0.8159 (m-70) cc_final: 0.7538 (m-70) REVERT: d 71 LEU cc_start: 0.8759 (mt) cc_final: 0.8441 (mt) REVERT: d 87 MET cc_start: 0.8564 (mtm) cc_final: 0.7847 (mtp) REVERT: d 196 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6987 (mt-10) REVERT: d 198 TYR cc_start: 0.7882 (m-80) cc_final: 0.7670 (m-80) REVERT: e 88 ARG cc_start: 0.7374 (mtt-85) cc_final: 0.7021 (mmt180) REVERT: e 141 LEU cc_start: 0.9195 (mm) cc_final: 0.8466 (tp) REVERT: e 144 LEU cc_start: 0.9155 (mt) cc_final: 0.8947 (mt) REVERT: e 147 LEU cc_start: 0.8962 (mt) cc_final: 0.8667 (mt) REVERT: e 149 ARG cc_start: 0.8992 (mtm-85) cc_final: 0.8497 (mtp85) REVERT: e 152 ASP cc_start: 0.8843 (m-30) cc_final: 0.8338 (m-30) REVERT: f 5 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7295 (tm-30) REVERT: f 19 LYS cc_start: 0.8712 (mtmm) cc_final: 0.7891 (mttm) REVERT: f 27 ASN cc_start: 0.9359 (m-40) cc_final: 0.9151 (m-40) REVERT: f 62 ILE cc_start: 0.8194 (mp) cc_final: 0.7268 (mp) REVERT: g 11 ASP cc_start: 0.7722 (p0) cc_final: 0.7205 (p0) REVERT: g 17 ILE cc_start: 0.8775 (pt) cc_final: 0.7948 (pt) REVERT: g 28 ASN cc_start: 0.8776 (m-40) cc_final: 0.8506 (m-40) REVERT: g 31 MET cc_start: 0.8915 (ttm) cc_final: 0.8438 (ttp) REVERT: g 57 ASP cc_start: 0.8084 (m-30) cc_final: 0.7679 (t70) REVERT: g 61 VAL cc_start: 0.9179 (t) cc_final: 0.8931 (t) REVERT: g 68 ASN cc_start: 0.9314 (m-40) cc_final: 0.9034 (m-40) REVERT: g 70 MET cc_start: 0.8779 (tmm) cc_final: 0.8543 (tmm) REVERT: g 96 ARG cc_start: 0.8473 (mtt90) cc_final: 0.8138 (mtt-85) REVERT: g 122 ASN cc_start: 0.8766 (m-40) cc_final: 0.8392 (m110) REVERT: g 130 ASN cc_start: 0.8784 (p0) cc_final: 0.8250 (p0) REVERT: g 135 VAL cc_start: 0.9406 (m) cc_final: 0.9115 (p) REVERT: h 46 ILE cc_start: 0.9028 (mm) cc_final: 0.8697 (mm) REVERT: h 98 LEU cc_start: 0.9189 (mt) cc_final: 0.8778 (mt) REVERT: h 101 LEU cc_start: 0.9207 (tt) cc_final: 0.8909 (tt) REVERT: h 127 VAL cc_start: 0.8862 (t) cc_final: 0.8490 (t) REVERT: i 13 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8712 (mttt) REVERT: i 28 ILE cc_start: 0.9206 (mp) cc_final: 0.8711 (mp) REVERT: i 34 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7457 (mm-30) REVERT: i 96 THR cc_start: 0.8401 (p) cc_final: 0.8061 (p) REVERT: i 103 LEU cc_start: 0.8310 (mt) cc_final: 0.8101 (mt) REVERT: j 10 LEU cc_start: 0.9068 (mm) cc_final: 0.8811 (mm) REVERT: j 63 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8310 (mt-10) REVERT: j 65 PHE cc_start: 0.8635 (m-80) cc_final: 0.8360 (m-80) REVERT: j 90 LEU cc_start: 0.9300 (mt) cc_final: 0.9045 (mt) REVERT: k 54 PHE cc_start: 0.7881 (m-80) cc_final: 0.7628 (m-80) REVERT: k 63 PHE cc_start: 0.8257 (t80) cc_final: 0.7769 (t80) REVERT: k 67 MET cc_start: 0.8238 (mpp) cc_final: 0.7570 (mpp) REVERT: k 83 THR cc_start: 0.9225 (p) cc_final: 0.8918 (p) REVERT: k 88 VAL cc_start: 0.9385 (t) cc_final: 0.9100 (m) REVERT: k 99 ILE cc_start: 0.8775 (mm) cc_final: 0.8555 (mm) REVERT: l 35 HIS cc_start: 0.7909 (m-70) cc_final: 0.7243 (m90) REVERT: l 128 SER cc_start: 0.8675 (p) cc_final: 0.8463 (p) REVERT: m 55 LYS cc_start: 0.9286 (ptmt) cc_final: 0.9062 (tmtt) REVERT: m 76 ASN cc_start: 0.8770 (m110) cc_final: 0.8517 (m-40) REVERT: m 87 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8219 (ttt90) REVERT: m 100 GLN cc_start: 0.8829 (mp10) cc_final: 0.8503 (mp10) REVERT: n 6 MET cc_start: 0.8582 (tpp) cc_final: 0.7978 (tpp) REVERT: n 18 VAL cc_start: 0.9378 (m) cc_final: 0.9155 (t) REVERT: n 21 TYR cc_start: 0.8587 (p90) cc_final: 0.7256 (p90) REVERT: n 39 LEU cc_start: 0.9134 (mt) cc_final: 0.8425 (tp) REVERT: o 7 ARG cc_start: 0.8716 (tpt90) cc_final: 0.7708 (tpt90) REVERT: o 11 LEU cc_start: 0.9263 (mt) cc_final: 0.8379 (mt) REVERT: o 43 LEU cc_start: 0.9417 (mm) cc_final: 0.9029 (mt) REVERT: o 54 ARG cc_start: 0.8616 (ttt90) cc_final: 0.8161 (ttt90) REVERT: o 78 TYR cc_start: 0.8718 (t80) cc_final: 0.8466 (t80) REVERT: p 6 ARG cc_start: 0.9035 (ptt180) cc_final: 0.8410 (ptt90) REVERT: p 19 ARG cc_start: 0.9007 (ttm170) cc_final: 0.8591 (ttm-80) REVERT: p 65 LYS cc_start: 0.8847 (mttt) cc_final: 0.8411 (mttm) REVERT: p 79 ILE cc_start: 0.8862 (mp) cc_final: 0.8522 (mp) REVERT: p 83 PHE cc_start: 0.8844 (t80) cc_final: 0.8386 (t80) REVERT: q 19 MET cc_start: 0.7537 (mpp) cc_final: 0.7202 (mmp) REVERT: q 41 LYS cc_start: 0.8755 (pttt) cc_final: 0.8027 (ptpp) REVERT: q 56 LYS cc_start: 0.7995 (mttt) cc_final: 0.7749 (mmtt) REVERT: r 33 LEU cc_start: 0.9528 (mt) cc_final: 0.8605 (mt) REVERT: r 35 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8981 (mtmm) REVERT: r 36 LYS cc_start: 0.9298 (mtmm) cc_final: 0.8989 (mttp) REVERT: r 43 LYS cc_start: 0.8396 (mtmm) cc_final: 0.7987 (mttp) REVERT: r 45 LEU cc_start: 0.8992 (mt) cc_final: 0.8514 (mt) REVERT: r 48 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7704 (mtt180) REVERT: r 56 TYR cc_start: 0.7956 (m-80) cc_final: 0.7665 (m-10) REVERT: r 66 ARG cc_start: 0.9247 (ptp-170) cc_final: 0.8965 (ptp-170) REVERT: r 75 TYR cc_start: 0.8185 (m-80) cc_final: 0.7502 (m-80) REVERT: t 48 LYS cc_start: 0.9511 (mptt) cc_final: 0.9294 (mmtt) REVERT: t 49 THR cc_start: 0.9682 (p) cc_final: 0.9412 (p) REVERT: t 60 LYS cc_start: 0.8827 (mttt) cc_final: 0.7994 (ttmm) REVERT: x 595 LEU cc_start: 0.9380 (mt) cc_final: 0.9118 (mt) REVERT: x 598 ARG cc_start: 0.8035 (ptt90) cc_final: 0.7593 (ppt170) REVERT: x 658 ASN cc_start: 0.8660 (m-40) cc_final: 0.8332 (m-40) REVERT: x 700 THR cc_start: 0.9007 (p) cc_final: 0.8329 (p) outliers start: 2 outliers final: 0 residues processed: 1976 average time/residue: 1.3019 time to fit residues: 4415.3491 Evaluate side-chains 1626 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1626 time to evaluate : 5.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 909 optimal weight: 7.9990 chunk 599 optimal weight: 10.0000 chunk 964 optimal weight: 20.0000 chunk 588 optimal weight: 5.9990 chunk 457 optimal weight: 3.9990 chunk 670 optimal weight: 10.0000 chunk 1012 optimal weight: 30.0000 chunk 931 optimal weight: 30.0000 chunk 806 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 622 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 62 ASN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 ASN K 4 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS P 2 GLN ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 4 ASN ** 2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 85 GLN c 68 HIS c 118 ASN c 122 GLN ** c 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 HIS ** d 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 HIS ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 ASN l 88 GLN m 32 GLN ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 HIS s 69 HIS t 68 HIS t 70 ASN ** x 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 159537 Z= 0.368 Angle : 0.803 15.568 238979 Z= 0.403 Chirality : 0.042 0.388 30585 Planarity : 0.006 0.125 12519 Dihedral : 25.332 179.935 80645 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.66 % Favored : 87.18 % Rotamer: Outliers : 0.08 % Allowed : 0.46 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.96 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.11), residues: 5546 helix: -1.08 (0.12), residues: 1641 sheet: -1.27 (0.18), residues: 859 loop : -2.49 (0.10), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP b 96 HIS 0.015 0.002 HIS C 53 PHE 0.033 0.003 PHE k 63 TYR 0.030 0.003 TYR D 46 ARG 0.018 0.001 ARG h 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11092 Ramachandran restraints generated. 5546 Oldfield, 0 Emsley, 5546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1910 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1906 time to evaluate : 6.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 SER cc_start: 0.8623 (p) cc_final: 0.8148 (m) REVERT: C 115 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 116 ILE cc_start: 0.8949 (mt) cc_final: 0.8727 (mt) REVERT: D 169 ILE cc_start: 0.8131 (mt) cc_final: 0.7882 (mm) REVERT: D 173 ASN cc_start: 0.7302 (t0) cc_final: 0.6730 (t0) REVERT: D 185 LEU cc_start: 0.9131 (mt) cc_final: 0.8775 (mp) REVERT: D 186 LEU cc_start: 0.9167 (mt) cc_final: 0.8702 (mt) REVERT: E 40 GLN cc_start: 0.8854 (tt0) cc_final: 0.8390 (tt0) REVERT: E 184 LEU cc_start: 0.9270 (pp) cc_final: 0.8760 (pp) REVERT: E 185 ASP cc_start: 0.8812 (m-30) cc_final: 0.8542 (m-30) REVERT: E 200 GLU cc_start: 0.9122 (mp0) cc_final: 0.8910 (mp0) REVERT: F 81 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8113 (mm-30) REVERT: F 138 PHE cc_start: 0.7151 (p90) cc_final: 0.6669 (p90) REVERT: F 154 ILE cc_start: 0.8351 (mm) cc_final: 0.8140 (mm) REVERT: F 170 LEU cc_start: 0.8956 (mt) cc_final: 0.8481 (mt) REVERT: G 75 ASN cc_start: 0.8886 (m110) cc_final: 0.8476 (t0) REVERT: G 84 PHE cc_start: 0.8638 (m-80) cc_final: 0.8226 (m-80) REVERT: J 93 MET cc_start: 0.8147 (mtt) cc_final: 0.7887 (mmt) REVERT: J 119 MET cc_start: 0.8457 (mtm) cc_final: 0.8227 (mtp) REVERT: K 2 ILE cc_start: 0.8516 (mt) cc_final: 0.8106 (mm) REVERT: K 5 GLU cc_start: 0.8670 (mp0) cc_final: 0.8030 (mp0) REVERT: K 54 LYS cc_start: 0.8023 (tttp) cc_final: 0.7672 (ttpt) REVERT: K 91 LYS cc_start: 0.8497 (mtpt) cc_final: 0.8275 (mttt) REVERT: L 23 ILE cc_start: 0.7517 (pt) cc_final: 0.7102 (tp) REVERT: M 44 ASN cc_start: 0.8571 (p0) cc_final: 0.8304 (p0) REVERT: M 59 LYS cc_start: 0.9242 (tmtt) cc_final: 0.8996 (tptp) REVERT: M 74 TYR cc_start: 0.8239 (p90) cc_final: 0.7628 (p90) REVERT: M 124 LYS cc_start: 0.9242 (mmpt) cc_final: 0.8813 (mmmt) REVERT: N 59 ARG cc_start: 0.8388 (tpp80) cc_final: 0.7746 (tpp80) REVERT: N 77 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8672 (tp-100) REVERT: N 81 GLN cc_start: 0.8348 (mt0) cc_final: 0.8010 (mt0) REVERT: N 82 LYS cc_start: 0.8763 (tttm) cc_final: 0.8244 (tttt) REVERT: N 95 GLN cc_start: 0.8433 (mt0) cc_final: 0.7979 (mp10) REVERT: N 116 ILE cc_start: 0.8483 (mt) cc_final: 0.8147 (mm) REVERT: N 118 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6533 (tm-30) REVERT: O 38 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8615 (mmtp) REVERT: O 58 THR cc_start: 0.8488 (p) cc_final: 0.8119 (p) REVERT: O 118 LEU cc_start: 0.9213 (mm) cc_final: 0.8912 (mm) REVERT: P 48 ILE cc_start: 0.8753 (mt) cc_final: 0.8551 (pt) REVERT: P 85 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7152 (mm-30) REVERT: P 101 ARG cc_start: 0.7337 (mtt180) cc_final: 0.6674 (mmt90) REVERT: Q 37 GLN cc_start: 0.7272 (mt0) cc_final: 0.6054 (tm-30) REVERT: Q 45 TYR cc_start: 0.8626 (m-10) cc_final: 0.8078 (m-10) REVERT: Q 61 TRP cc_start: 0.9162 (m-10) cc_final: 0.8474 (m-90) REVERT: R 28 GLU cc_start: 0.8940 (pp20) cc_final: 0.8688 (pp20) REVERT: R 69 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8321 (tppt) REVERT: R 92 TYR cc_start: 0.8513 (p90) cc_final: 0.8299 (p90) REVERT: S 48 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8214 (mt-10) REVERT: S 106 VAL cc_start: 0.8433 (t) cc_final: 0.7384 (t) REVERT: T 3 ASP cc_start: 0.8632 (p0) cc_final: 0.8387 (p0) REVERT: T 13 ILE cc_start: 0.9212 (mp) cc_final: 0.8718 (tp) REVERT: T 21 MET cc_start: 0.8903 (mtm) cc_final: 0.8125 (mtt) REVERT: T 28 PHE cc_start: 0.8010 (m-80) cc_final: 0.7717 (m-80) REVERT: T 57 MET cc_start: 0.7081 (mtp) cc_final: 0.6796 (mtp) REVERT: U 1 MET cc_start: 0.7442 (mtt) cc_final: 0.6356 (mpp) REVERT: U 9 VAL cc_start: 0.9145 (t) cc_final: 0.8890 (p) REVERT: U 64 HIS cc_start: 0.8588 (t-90) cc_final: 0.7844 (t-170) REVERT: U 99 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8491 (mm-40) REVERT: V 19 LYS cc_start: 0.8834 (tppt) cc_final: 0.7910 (tptp) REVERT: V 22 ARG cc_start: 0.7868 (pmt170) cc_final: 0.6885 (pmt170) REVERT: V 37 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8717 (mm-40) REVERT: V 46 TYR cc_start: 0.7817 (t80) cc_final: 0.7592 (t80) REVERT: V 68 PHE cc_start: 0.8310 (p90) cc_final: 0.8077 (p90) REVERT: X 28 LEU cc_start: 0.9261 (mm) cc_final: 0.8979 (tp) REVERT: X 43 ILE cc_start: 0.9301 (mp) cc_final: 0.9067 (mp) REVERT: Y 29 LYS cc_start: 0.8611 (mppt) cc_final: 0.8095 (mppt) REVERT: Y 30 LYS cc_start: 0.8824 (mttt) cc_final: 0.8411 (mmmt) REVERT: Y 38 GLU cc_start: 0.8207 (pp20) cc_final: 0.7772 (pp20) REVERT: 1 21 LYS cc_start: 0.7235 (pttt) cc_final: 0.6303 (mmtm) REVERT: 2 6 THR cc_start: 0.9007 (p) cc_final: 0.8755 (p) REVERT: 2 12 CYS cc_start: 0.6067 (t) cc_final: 0.5779 (t) REVERT: 2 44 LEU cc_start: 0.9013 (tp) cc_final: 0.8543 (tt) REVERT: 3 1 MET cc_start: 0.4936 (mmm) cc_final: 0.4568 (mmp) REVERT: 3 28 ARG cc_start: 0.7477 (mpp80) cc_final: 0.7095 (mtt-85) REVERT: 4 23 LYS cc_start: 0.7188 (tmmt) cc_final: 0.6916 (pttp) REVERT: 4 35 ASN cc_start: 0.8517 (m-40) cc_final: 0.8093 (m-40) REVERT: 5 1 MET cc_start: 0.8994 (tpp) cc_final: 0.8664 (tpp) REVERT: 5 18 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7875 (tpp80) REVERT: b 27 MET cc_start: 0.8025 (mpp) cc_final: 0.7732 (mpp) REVERT: b 45 LYS cc_start: 0.9471 (mtmt) cc_final: 0.9212 (mtmt) REVERT: b 86 ARG cc_start: 0.8496 (ptm160) cc_final: 0.7962 (ptt90) REVERT: b 177 ARG cc_start: 0.8814 (ttt90) cc_final: 0.8476 (ttm170) REVERT: b 178 LYS cc_start: 0.8535 (ttmt) cc_final: 0.7899 (tptm) REVERT: c 31 PHE cc_start: 0.8550 (m-80) cc_final: 0.8024 (m-80) REVERT: c 35 ASP cc_start: 0.8012 (t70) cc_final: 0.7810 (t70) REVERT: c 88 LYS cc_start: 0.9312 (ptpp) cc_final: 0.8929 (ptpp) REVERT: c 101 ASN cc_start: 0.8219 (t0) cc_final: 0.8005 (t0) REVERT: c 182 ASP cc_start: 0.8021 (t70) cc_final: 0.7597 (t0) REVERT: d 47 TYR cc_start: 0.8673 (t80) cc_final: 0.8153 (t80) REVERT: d 50 GLN cc_start: 0.9264 (mt0) cc_final: 0.8417 (mm-40) REVERT: d 59 HIS cc_start: 0.8179 (m-70) cc_final: 0.7561 (m-70) REVERT: d 67 GLN cc_start: 0.8322 (tp-100) cc_final: 0.8119 (tp-100) REVERT: d 71 LEU cc_start: 0.8780 (mt) cc_final: 0.8478 (mt) REVERT: d 196 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6981 (mt-10) REVERT: d 198 TYR cc_start: 0.8016 (m-80) cc_final: 0.7605 (m-10) REVERT: e 149 ARG cc_start: 0.9087 (mtm-85) cc_final: 0.8604 (ttm-80) REVERT: e 152 ASP cc_start: 0.8843 (m-30) cc_final: 0.8549 (m-30) REVERT: f 5 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7820 (tm-30) REVERT: f 19 LYS cc_start: 0.8696 (mtmm) cc_final: 0.7861 (mttm) REVERT: f 27 ASN cc_start: 0.9320 (m-40) cc_final: 0.9090 (m-40) REVERT: f 51 GLU cc_start: 0.8504 (tp30) cc_final: 0.7972 (tm-30) REVERT: f 55 PHE cc_start: 0.6999 (m-10) cc_final: 0.6637 (m-10) REVERT: f 61 GLN cc_start: 0.7589 (mp10) cc_final: 0.7286 (mp10) REVERT: f 62 ILE cc_start: 0.8158 (mp) cc_final: 0.7944 (mp) REVERT: f 82 SER cc_start: 0.8116 (p) cc_final: 0.7856 (t) REVERT: g 11 ASP cc_start: 0.7732 (p0) cc_final: 0.7179 (p0) REVERT: g 28 ASN cc_start: 0.8775 (m-40) cc_final: 0.8488 (m-40) REVERT: g 31 MET cc_start: 0.8943 (ttm) cc_final: 0.8514 (ttt) REVERT: g 68 ASN cc_start: 0.9319 (m-40) cc_final: 0.9034 (m-40) REVERT: g 70 MET cc_start: 0.8837 (tmm) cc_final: 0.8573 (tmm) REVERT: g 122 ASN cc_start: 0.8856 (m-40) cc_final: 0.8445 (m110) REVERT: g 130 ASN cc_start: 0.8839 (p0) cc_final: 0.8296 (p0) REVERT: g 135 VAL cc_start: 0.9445 (m) cc_final: 0.9150 (p) REVERT: h 39 ILE cc_start: 0.9459 (tt) cc_final: 0.9252 (tt) REVERT: h 46 ILE cc_start: 0.9021 (mm) cc_final: 0.8759 (mm) REVERT: h 64 LEU cc_start: 0.8819 (mm) cc_final: 0.8252 (mt) REVERT: h 98 LEU cc_start: 0.9233 (mt) cc_final: 0.8744 (mt) REVERT: h 101 LEU cc_start: 0.9247 (tt) cc_final: 0.8947 (tt) REVERT: i 13 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8819 (ttmt) REVERT: i 96 THR cc_start: 0.8807 (p) cc_final: 0.8096 (p) REVERT: j 10 LEU cc_start: 0.9077 (mm) cc_final: 0.8791 (mm) REVERT: j 90 LEU cc_start: 0.9386 (mt) cc_final: 0.9087 (mt) REVERT: k 54 PHE cc_start: 0.7989 (m-80) cc_final: 0.7722 (m-80) REVERT: k 63 PHE cc_start: 0.8306 (t80) cc_final: 0.7820 (t80) REVERT: k 67 MET cc_start: 0.8229 (mpp) cc_final: 0.7623 (mpp) REVERT: k 88 VAL cc_start: 0.9433 (t) cc_final: 0.9122 (m) REVERT: k 128 ARG cc_start: 0.8313 (ttm170) cc_final: 0.8000 (mtp180) REVERT: l 35 HIS cc_start: 0.7990 (m-70) cc_final: 0.7327 (m90) REVERT: l 128 SER cc_start: 0.8717 (p) cc_final: 0.8495 (p) REVERT: m 31 GLN cc_start: 0.9368 (mt0) cc_final: 0.8950 (mt0) REVERT: m 55 LYS cc_start: 0.9309 (ptmt) cc_final: 0.9018 (tttt) REVERT: m 76 ASN cc_start: 0.8804 (m110) cc_final: 0.8561 (m-40) REVERT: m 100 GLN cc_start: 0.8863 (mp10) cc_final: 0.8439 (mp10) REVERT: n 6 MET cc_start: 0.8750 (tpp) cc_final: 0.8380 (tpp) REVERT: n 9 LYS cc_start: 0.8578 (ttpt) cc_final: 0.8369 (tttt) REVERT: n 35 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.7812 (ttm-80) REVERT: n 39 LEU cc_start: 0.9246 (mt) cc_final: 0.8424 (tp) REVERT: o 7 ARG cc_start: 0.8681 (tpt90) cc_final: 0.7892 (tpt90) REVERT: o 11 LEU cc_start: 0.9469 (mt) cc_final: 0.8433 (mt) REVERT: o 43 LEU cc_start: 0.9474 (mm) cc_final: 0.9099 (mt) REVERT: o 54 ARG cc_start: 0.8660 (ttt90) cc_final: 0.8397 (ttt90) REVERT: o 78 TYR cc_start: 0.8802 (t80) cc_final: 0.8512 (t80) REVERT: p 6 ARG cc_start: 0.9115 (ptt180) cc_final: 0.8423 (ptt90) REVERT: p 19 ARG cc_start: 0.9034 (ttm170) cc_final: 0.8699 (ttm170) REVERT: p 25 SER cc_start: 0.9262 (p) cc_final: 0.8848 (p) REVERT: p 65 LYS cc_start: 0.8812 (mttt) cc_final: 0.8449 (mttm) REVERT: p 83 PHE cc_start: 0.8876 (t80) cc_final: 0.8443 (t80) REVERT: q 19 MET cc_start: 0.7363 (mpp) cc_final: 0.7000 (mmp) REVERT: q 41 LYS cc_start: 0.8712 (pttt) cc_final: 0.8257 (ptpt) REVERT: q 56 LYS cc_start: 0.7995 (mttt) cc_final: 0.7702 (mmtt) REVERT: q 65 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7829 (tm-30) REVERT: r 33 LEU cc_start: 0.9547 (mt) cc_final: 0.9244 (mt) REVERT: r 43 LYS cc_start: 0.8341 (mtmm) cc_final: 0.7962 (mttp) REVERT: r 45 LEU cc_start: 0.9031 (mt) cc_final: 0.8561 (mt) REVERT: r 48 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7814 (mtt180) REVERT: r 75 TYR cc_start: 0.8271 (m-80) cc_final: 0.7585 (m-80) REVERT: s 20 GLU cc_start: 0.8892 (tp30) cc_final: 0.8516 (tp30) REVERT: s 24 GLU cc_start: 0.9002 (pt0) cc_final: 0.8463 (pt0) REVERT: t 48 LYS cc_start: 0.9496 (mptt) cc_final: 0.9245 (mmtt) REVERT: t 49 THR cc_start: 0.9685 (p) cc_final: 0.9409 (p) REVERT: t 60 LYS cc_start: 0.8866 (mttt) cc_final: 0.7986 (ttmm) REVERT: x 595 LEU cc_start: 0.9369 (mt) cc_final: 0.9103 (mt) REVERT: x 658 ASN cc_start: 0.8751 (m-40) cc_final: 0.8389 (m-40) REVERT: x 700 THR cc_start: 0.9005 (p) cc_final: 0.8245 (p) outliers start: 4 outliers final: 3 residues processed: 1908 average time/residue: 1.2970 time to fit residues: 4253.9055 Evaluate side-chains 1627 residues out of total 4748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1624 time to evaluate : 6.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 494 optimal weight: 9.9990 chunk 640 optimal weight: 20.0000 chunk 858 optimal weight: 5.9990 chunk 246 optimal weight: 20.0000 chunk 743 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 223 optimal weight: 8.9990 chunk 807 optimal weight: 10.0000 chunk 337 optimal weight: 6.9990 chunk 828 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN K 4 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS P 2 GLN ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 ASN Q 81 HIS Q 116 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 4 ASN ** 2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 122 GLN ** c 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 GLN ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 85 HIS l 86 ASN m 32 GLN ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 83 ASN ** p 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS t 68 HIS ** t 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083043 restraints weight = 427515.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083353 restraints weight = 231403.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.083987 restraints weight = 186595.996| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 159537 Z= 0.423 Angle : 0.869 17.294 238979 Z= 0.433 Chirality : 0.045 0.397 30585 Planarity : 0.007 0.156 12519 Dihedral : 25.496 179.649 80645 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 30.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.09 % Favored : 86.75 % Rotamer: Outliers : 0.06 % Allowed : 0.63 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.96 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.10), residues: 5546 helix: -1.27 (0.12), residues: 1647 sheet: -1.35 (0.18), residues: 841 loop : -2.59 (0.10), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP b 96 HIS 0.018 0.002 HIS C 53 PHE 0.039 0.003 PHE s 44 TYR 0.036 0.003 TYR g 85 ARG 0.020 0.001 ARG j 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 56776.82 seconds wall clock time: 982 minutes 52.31 seconds (58972.31 seconds total)