Starting phenix.real_space_refine on Tue Mar 19 19:07:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha1_0176/03_2024/6ha1_0176_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha1_0176/03_2024/6ha1_0176.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha1_0176/03_2024/6ha1_0176_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha1_0176/03_2024/6ha1_0176_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha1_0176/03_2024/6ha1_0176_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha1_0176/03_2024/6ha1_0176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha1_0176/03_2024/6ha1_0176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha1_0176/03_2024/6ha1_0176_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ha1_0176/03_2024/6ha1_0176_neut_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.011 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 4618 5.49 5 S 133 5.16 5 C 70330 2.51 5 N 26163 2.21 5 O 39580 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 PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "F ARG 125": "NH1" <-> "NH2" 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 TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 84": "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 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "3 TYR 28": "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 PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "d TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "d TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 146": "NH1" <-> "NH2" Residue "d PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "i TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" 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" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 140824 Number of models: 1 Model: "" Number of chains: 52 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': 295, 'rna2p_pyr': 162, 'rna3p_pur': 1382, 'rna3p_pyr': 1047} 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: "W" 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: "X" 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: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "Z" 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: "0" 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: "1" 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: "2" 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: "3" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "4" 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: "6" 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: "7" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} 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: "x" 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: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'TEL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 49.20, per 1000 atoms: 0.35 Number of scatterers: 140824 At special positions: 0 Unit cell: (268.433, 275.86, 221.749, 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 133 16.00 P 4618 15.00 O 39580 8.00 N 26163 7.00 C 70330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 0 30 " - pdb=" SG CYS 0 43 " distance=2.03 Simple disulfide: pdb=" SG CYS 0 33 " - pdb=" SG CYS 0 46 " distance=2.03 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: 57.35 Conformation dependent library (CDL) restraints added in 5.5 seconds 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9698 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 155 helices and 67 sheets defined 37.3% alpha, 19.1% beta 1460 base pairs and 2666 stacking pairs defined. Time for finding SS restraints: 72.58 Creating SS restraints... Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.299A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.859A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.801A pdb=" N ILE C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.767A pdb=" N SER D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.539A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 92' Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'E' and resid 29 through 46 removed outlier: 3.726A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.844A pdb=" N MET E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 169 removed outlier: 4.554A pdb=" N ALA E 167 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 4.175A pdb=" N VAL E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'F' and resid 2 through 21 removed outlier: 3.543A pdb=" N GLU F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) Proline residue: F 14 - end of helix Processing helix chain 'F' and resid 48 through 62 removed outlier: 4.321A pdb=" N SER F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR F 58 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY F 62 " --> pdb=" O THR F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 4.341A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 112 removed outlier: 4.609A pdb=" N ARG F 110 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 112' Processing helix chain 'F' and resid 142 through 147 removed outlier: 5.110A pdb=" N THR F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.170A pdb=" N ALA F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 4.472A pdb=" N ALA F 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN F 45 " --> pdb=" O ASP F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.747A pdb=" N ALA G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG G 70 " --> pdb=" O HIS G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 154 removed outlier: 4.153A pdb=" N ALA G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 39 removed outlier: 3.803A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 97 removed outlier: 3.751A pdb=" N ASN J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 111 Proline residue: J 111 - end of helix Processing helix chain 'J' and resid 113 through 123 removed outlier: 3.936A pdb=" N LYS J 122 " --> pdb=" O GLN J 118 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU J 123 " --> pdb=" O MET J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 3.843A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 110' Processing helix chain 'K' and resid 111 through 118 removed outlier: 3.642A pdb=" N LEU K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.577A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 78 through 85 removed outlier: 6.621A pdb=" N LEU L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 92 through 100 Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.704A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 removed outlier: 3.725A pdb=" N ILE M 47 " --> pdb=" O THR M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.965A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 9 through 28 Processing helix chain 'N' and resid 34 through 54 removed outlier: 4.414A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG N 53 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 66 removed outlier: 3.766A pdb=" N ARG N 59 " --> pdb=" O ASP N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 92 removed outlier: 3.625A pdb=" N SER N 85 " --> pdb=" O GLN N 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 22 removed outlier: 3.764A pdb=" N ALA O 10 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA O 20 " --> pdb=" O ALA O 16 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS O 21 " --> pdb=" O ARG O 17 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU O 22 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 89 removed outlier: 4.178A pdb=" N GLY O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 117 Processing helix chain 'P' and resid 1 through 14 removed outlier: 5.150A pdb=" N GLU P 11 " --> pdb=" O ASP P 7 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLN P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG P 14 " --> pdb=" O LYS P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.826A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 5.268A pdb=" N THR Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG Q 11 " --> pdb=" O GLY Q 7 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 31 removed outlier: 4.854A pdb=" N HIS Q 29 " --> pdb=" O PHE Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.526A pdb=" N ARG Q 51 " --> pdb=" O PHE Q 47 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N MET Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 92 through 103 Processing helix chain 'Q' and resid 104 through 118 removed outlier: 3.695A pdb=" N GLN Q 108 " --> pdb=" O THR Q 104 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.690A pdb=" N ALA S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 4.028A pdb=" N LEU S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR S 39 " --> pdb=" O ILE S 35 " (cutoff:3.500A) Proline residue: S 40 - end of helix Processing helix chain 'S' and resid 41 through 61 Proline residue: S 45 - end of helix Processing helix chain 'S' and resid 65 through 70 removed outlier: 4.233A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL S 70 " --> pdb=" O ALA S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 3 through 9 removed outlier: 4.013A pdb=" N VAL T 7 " --> pdb=" O ASP T 3 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU T 8 " --> pdb=" O PRO T 4 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS T 9 " --> pdb=" O ARG T 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3 through 9' Processing helix chain 'T' and resid 14 through 24 removed outlier: 3.513A pdb=" N GLU T 23 " --> pdb=" O ASP T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 47 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.351A pdb=" N VAL U 68 " --> pdb=" O HIS U 64 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N MET U 69 " --> pdb=" O VAL U 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 64 through 69' Processing helix chain 'X' and resid 50 through 55 removed outlier: 4.332A pdb=" N LYS X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 9 removed outlier: 4.698A pdb=" N ASP Y 8 " --> pdb=" O ASN Y 4 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 35 Processing helix chain 'Y' and resid 39 through 65 removed outlier: 4.144A pdb=" N ILE Y 43 " --> pdb=" O ASN Y 39 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG Y 44 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE Y 57 " --> pdb=" O MET Y 53 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.972A pdb=" N GLY Z 27 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 9 through 21 removed outlier: 5.101A pdb=" N HIS 0 19 " --> pdb=" O LEU 0 15 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '1' and resid 22 through 27 Proline residue: 1 27 - end of helix No H-bonds generated for 'chain '1' and resid 22 through 27' Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.200A pdb=" N SER 2 24 " --> pdb=" O SER 2 20 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 removed outlier: 3.848A pdb=" N GLY 2 38 " --> pdb=" O ARG 2 34 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 14 Processing helix chain '3' and resid 32 through 37 removed outlier: 4.592A pdb=" N LYS 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER 3 37 " --> pdb=" O PHE 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 46 removed outlier: 4.293A pdb=" N LYS 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 5.550A pdb=" N GLN 3 60 " --> pdb=" O LYS 3 56 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N MET 3 61 " --> pdb=" O ARG 3 57 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU 3 62 " --> pdb=" O ILE 3 58 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA 3 63 " --> pdb=" O LYS 3 59 " (cutoff:3.500A) Processing helix chain '4' and resid 29 through 34 removed outlier: 3.787A pdb=" N LYS 4 33 " --> pdb=" O ASN 4 29 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN 4 34 " --> pdb=" O PRO 4 30 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 29 through 34' Processing helix chain '6' and resid 36 through 41 Proline residue: 6 41 - end of helix Processing helix chain '6' and resid 49 through 54 Processing helix chain 'b' and resid 24 through 29 removed outlier: 4.704A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ARG b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 29' Processing helix chain 'b' and resid 42 through 64 removed outlier: 3.502A pdb=" N THR b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS b 49 " --> pdb=" O LYS b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 88 removed outlier: 4.709A pdb=" N ASP b 78 " --> pdb=" O LYS b 74 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER b 79 " --> pdb=" O GLN b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 123 removed outlier: 3.645A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU b 122 " --> pdb=" O GLU b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 148 removed outlier: 4.550A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG b 143 " --> pdb=" O LYS b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 192 through 197 removed outlier: 3.986A pdb=" N ILE b 196 " --> pdb=" O ASP b 192 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP b 197 " --> pdb=" O PRO b 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 192 through 197' Processing helix chain 'b' and resid 206 through 225 removed outlier: 3.768A pdb=" N ALA b 224 " --> pdb=" O ALA b 220 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS b 225 " --> pdb=" O ILE b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 149 through 154 removed outlier: 4.090A pdb=" N LYS b 152 " --> pdb=" O GLY b 149 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP b 153 " --> pdb=" O GLY b 150 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET b 154 " --> pdb=" O ILE b 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 149 through 154' Processing helix chain 'c' and resid 6 through 12 Processing helix chain 'c' and resid 27 through 50 removed outlier: 4.502A pdb=" N ASP c 48 " --> pdb=" O LYS c 44 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA c 49 " --> pdb=" O ARG c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 76 removed outlier: 4.687A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 78 through 95 removed outlier: 6.452A pdb=" N GLU c 82 " --> pdb=" O LYS c 78 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL c 83 " --> pdb=" O GLY c 79 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA c 89 " --> pdb=" O ALA c 85 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU c 90 " --> pdb=" O LEU c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.537A pdb=" N GLN c 122 " --> pdb=" O ASN c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 4.274A pdb=" N GLN c 133 " --> pdb=" O PHE c 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 6.213A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER d 12 " --> pdb=" O SER d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 Processing helix chain 'd' and resid 64 through 79 removed outlier: 4.991A pdb=" N ALA d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 94 removed outlier: 6.303A pdb=" N LEU d 94 " --> pdb=" O LEU d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 95 through 102 Processing helix chain 'd' and resid 106 through 116 removed outlier: 3.734A pdb=" N ALA d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 158 removed outlier: 5.069A pdb=" N ASN d 158 " --> pdb=" O SER d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 186 removed outlier: 3.978A pdb=" N ALA d 186 " --> pdb=" O ARG d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 200 removed outlier: 4.352A pdb=" N ILE d 194 " --> pdb=" O ASN d 190 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU d 196 " --> pdb=" O ALA d 192 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 3.781A pdb=" N ALA e 59 " --> pdb=" O GLU e 55 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 removed outlier: 3.821A pdb=" N GLY e 119 " --> pdb=" O LEU e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 147 removed outlier: 3.963A pdb=" N LEU e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 removed outlier: 3.895A pdb=" N GLY e 158 " --> pdb=" O ALA e 154 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 166 removed outlier: 3.630A pdb=" N GLY e 166 " --> pdb=" O GLU e 162 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 34 removed outlier: 3.615A pdb=" N SER f 32 " --> pdb=" O ASN f 28 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN f 33 " --> pdb=" O VAL f 29 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY f 34 " --> pdb=" O LEU f 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 69 through 82 removed outlier: 4.974A pdb=" N GLN f 73 " --> pdb=" O ALA f 69 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.831A pdb=" N SER g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET g 30 " --> pdb=" O LEU g 26 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET g 31 " --> pdb=" O ILE g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.569A pdb=" N SER g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR g 54 " --> pdb=" O ILE g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.831A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 4.026A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.800A pdb=" N ASN g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN g 130 " --> pdb=" O ASP g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.987A pdb=" N LYS g 137 " --> pdb=" O ALA g 133 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.899A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.559A pdb=" N GLY h 44 " --> pdb=" O LEU h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 41 through 56 removed outlier: 4.024A pdb=" N ILE i 45 " --> pdb=" O SER i 41 " (cutoff:3.500A) Proline residue: i 51 - end of helix removed outlier: 3.657A pdb=" N THR i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU i 56 " --> pdb=" O LEU i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 92 Proline residue: i 92 - end of helix Processing helix chain 'i' and resid 94 through 102 Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.549A pdb=" N LEU j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.844A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 53 removed outlier: 3.940A pdb=" N GLY k 53 " --> pdb=" O ALA k 49 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 62 removed outlier: 3.958A pdb=" N THR k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix No H-bonds generated for 'chain 'k' and resid 57 through 62' Processing helix chain 'k' and resid 63 through 80 Processing helix chain 'k' and resid 94 through 106 removed outlier: 4.136A pdb=" N GLY k 106 " --> pdb=" O LEU k 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 21 through 27 removed outlier: 3.956A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS l 26 " --> pdb=" O PRO l 22 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLY l 27 " --> pdb=" O ALA l 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 27' Processing helix chain 'l' and resid 126 through 131 removed outlier: 4.879A pdb=" N TYR l 130 " --> pdb=" O GLY l 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY l 131 " --> pdb=" O ARG l 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 126 through 131' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.926A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.697A pdb=" N ALA m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU m 36 " --> pdb=" O GLN m 32 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 64 removed outlier: 3.760A pdb=" N ILE m 56 " --> pdb=" O GLU m 52 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS m 64 " --> pdb=" O ILE m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 4.493A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.656A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 13 removed outlier: 4.934A pdb=" N MET n 6 " --> pdb=" O ALA n 2 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 21 removed outlier: 3.733A pdb=" N GLU n 20 " --> pdb=" O PHE n 16 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 16 through 21' Processing helix chain 'n' and resid 40 through 51 Processing helix chain 'o' and resid 4 through 16 removed outlier: 5.847A pdb=" N LYS o 8 " --> pdb=" O THR o 4 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN o 9 " --> pdb=" O GLN o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.164A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.074A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 52 through 63 removed outlier: 5.672A pdb=" N ALA p 56 " --> pdb=" O ASP p 52 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU p 57 " --> pdb=" O GLU p 53 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR p 62 " --> pdb=" O LYS p 58 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY p 63 " --> pdb=" O TRP p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 79 through 89 Processing helix chain 'r' and resid 16 through 22 removed outlier: 3.665A pdb=" N SER r 20 " --> pdb=" O CYS r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 39 removed outlier: 5.518A pdb=" N SER r 39 " --> pdb=" O LYS r 35 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 71 Processing helix chain 's' and resid 12 through 26 removed outlier: 4.116A pdb=" N THR s 25 " --> pdb=" O LYS s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.598A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 6 through 42 removed outlier: 4.986A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN t 42 " --> pdb=" O SER t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 Processing helix chain 't' and resid 68 through 86 removed outlier: 4.282A pdb=" N LEU t 86 " --> pdb=" O LYS t 82 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 6.662A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N THR C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.565A pdb=" N GLN C 163 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LYS C 170 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 91 through 96 removed outlier: 3.790A pdb=" N TYR C 96 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 3 through 8 removed outlier: 6.178A pdb=" N LYS D 3 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU D 167 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLY D 116 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLY D 165 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY D 118 " --> pdb=" O ARG D 163 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG D 163 " --> pdb=" O GLY D 118 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 11 through 17 removed outlier: 4.059A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASN D 184 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 37 through 41 removed outlier: 4.523A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 48 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR D 46 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 36 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 34 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLN D 95 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 48 through 54 Processing sheet with id= 9, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.502A pdb=" N VAL E 4 " --> pdb=" O ILE E 17 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.552A pdb=" N ILE E 194 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS E 191 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 86 through 92 removed outlier: 5.860A pdb=" N ALA F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 16 through 19 removed outlier: 5.464A pdb=" N ASN G 23 " --> pdb=" O PHE G 38 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 42 through 46 Processing sheet with id= 14, first strand: chain 'G' and resid 96 through 99 Processing sheet with id= 15, first strand: chain 'G' and resid 122 through 126 removed outlier: 5.998A pdb=" N THR G 130 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU G 90 " --> pdb=" O THR G 130 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL G 91 " --> pdb=" O GLY G 162 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 14 through 17 No H-bonds generated for sheet with id= 16 Processing sheet with id= 17, first strand: chain 'J' and resid 75 through 79 removed outlier: 6.336A pdb=" N GLY J 84 " --> pdb=" O THR J 79 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'K' and resid 6 through 9 removed outlier: 4.385A pdb=" N THR K 6 " --> pdb=" O THR K 21 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 38 through 42 Processing sheet with id= 20, first strand: chain 'K' and resid 63 through 66 removed outlier: 3.668A pdb=" N ARG K 64 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LYS K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.254A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 23, first strand: chain 'L' and resid 87 through 91 removed outlier: 6.543A pdb=" N LYS L 120 " --> pdb=" O GLU L 87 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR L 89 " --> pdb=" O LYS L 120 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL L 91 " --> pdb=" O THR L 122 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 63 through 66 removed outlier: 4.045A pdb=" N LYS M 63 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER M 107 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP M 65 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE M 34 " --> pdb=" O LEU M 103 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS M 101 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 73 through 77 removed outlier: 6.680A pdb=" N TYR M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA M 89 " --> pdb=" O ALA M 76 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 31 through 37 removed outlier: 8.292A pdb=" N GLU M 31 " --> pdb=" O ARG M 134 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.784A pdb=" N ARG N 107 " --> pdb=" O GLY N 111 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLY N 105 " --> pdb=" O PRO N 113 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA N 115 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS N 103 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE N 117 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE N 101 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU N 119 " --> pdb=" O THR N 99 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR N 99 " --> pdb=" O LEU N 119 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 54 through 57 removed outlier: 3.643A pdb=" N ALA O 54 " --> pdb=" O ILE O 44 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL O 33 " --> pdb=" O ASP O 96 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 40 through 45 Processing sheet with id= 30, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.830A pdb=" N LYS P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY P 53 " --> pdb=" O SER P 56 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER P 56 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N GLU P 57 " --> pdb=" O VAL P 76 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 2 through 6 Processing sheet with id= 32, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.923A pdb=" N GLN R 18 " --> pdb=" O ILE R 97 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS R 94 " --> pdb=" O GLU R 63 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLU R 63 " --> pdb=" O LYS R 94 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU R 98 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR R 59 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU R 31 " --> pdb=" O VAL R 62 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 64 through 67 removed outlier: 5.479A pdb=" N LYS R 64 " --> pdb=" O LYS R 94 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 70 through 77 removed outlier: 4.559A pdb=" N VAL R 82 " --> pdb=" O LYS R 77 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 2 through 8 removed outlier: 5.969A pdb=" N ILE S 103 " --> pdb=" O ALA S 7 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 80 through 88 removed outlier: 4.760A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG S 88 " --> pdb=" O ARG S 92 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 25 through 30 removed outlier: 3.919A pdb=" N ARG T 77 " --> pdb=" O VAL T 30 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS T 62 " --> pdb=" O THR T 73 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARG T 75 " --> pdb=" O LYS T 60 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS T 60 " --> pdb=" O ARG T 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG T 77 " --> pdb=" O ASN T 58 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN T 58 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA T 79 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE T 56 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL T 81 " --> pdb=" O VAL T 54 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL T 54 " --> pdb=" O VAL T 81 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 39 through 45 removed outlier: 4.974A pdb=" N ASN U 39 " --> pdb=" O ALA U 61 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY U 55 " --> pdb=" O SER U 45 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 80 through 83 removed outlier: 5.422A pdb=" N ARG U 80 " --> pdb=" O LYS U 95 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'W' and resid 37 through 40 removed outlier: 4.329A pdb=" N GLN W 37 " --> pdb=" O VAL W 75 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LYS W 86 " --> pdb=" O GLU W 78 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'X' and resid 11 through 16 removed outlier: 7.517A pdb=" N LYS X 11 " --> pdb=" O ALA X 31 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA X 31 " --> pdb=" O LYS X 11 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.524A pdb=" N ILE Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS Z 3 " --> pdb=" O GLN Z 59 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN Z 59 " --> pdb=" O LYS Z 3 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU Z 53 " --> pdb=" O LYS Z 9 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '1' and resid 3 through 7 removed outlier: 4.421A pdb=" N TYR 1 17 " --> pdb=" O LEU 1 7 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '1' and resid 30 through 36 removed outlier: 6.099A pdb=" N VAL 1 30 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS 1 41 " --> pdb=" O CYS 1 36 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '3' and resid 22 through 25 removed outlier: 5.509A pdb=" N LEU 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '6' and resid 20 through 25 removed outlier: 4.250A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU 6 29 " --> pdb=" O LYS 6 11 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR 6 13 " --> pdb=" O GLU 6 29 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL 6 31 " --> pdb=" O THR 6 13 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL 6 33 " --> pdb=" O LYS 6 15 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 89 through 92 removed outlier: 3.586A pdb=" N LEU b 68 " --> pdb=" O ALA b 160 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE b 164 " --> pdb=" O VAL b 70 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU b 161 " --> pdb=" O PRO b 182 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE b 186 " --> pdb=" O ILE b 163 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 52 through 58 removed outlier: 3.773A pdb=" N LYS c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN c 64 " --> pdb=" O GLU c 57 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE c 105 " --> pdb=" O THR c 69 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.739A pdb=" N GLY c 154 " --> pdb=" O ARG c 163 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 165 through 168 removed outlier: 3.611A pdb=" N ASP d 168 " --> pdb=" O GLU d 173 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU d 173 " --> pdb=" O ASP d 168 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 17 through 25 removed outlier: 3.733A pdb=" N THR e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 84 through 88 removed outlier: 6.446A pdb=" N ASP e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE e 123 " --> pdb=" O GLY e 104 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 39 through 43 removed outlier: 3.788A pdb=" N GLY f 39 " --> pdb=" O ASN f 64 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP f 43 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LYS f 3 " --> pdb=" O GLU f 93 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 44 through 48 removed outlier: 4.046A pdb=" N GLY f 44 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG f 56 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'g' and resid 72 through 79 No H-bonds generated for sheet with id= 55 Processing sheet with id= 56, first strand: chain 'h' and resid 23 through 27 removed outlier: 5.861A pdb=" N GLU h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'h' and resid 76 through 79 removed outlier: 4.652A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'i' and resid 5 through 11 removed outlier: 5.701A pdb=" N TYR i 61 " --> pdb=" O GLU i 25 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG i 27 " --> pdb=" O TYR i 61 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 42 through 52 removed outlier: 4.977A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS j 11 " --> pdb=" O ASP j 97 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP j 97 " --> pdb=" O LYS j 11 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 32 through 37 removed outlier: 3.590A pdb=" N GLY k 21 " --> pdb=" O THR k 83 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA k 23 " --> pdb=" O GLU k 85 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR k 110 " --> pdb=" O LEU k 84 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL k 86 " --> pdb=" O THR k 110 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'k' and resid 85 through 88 Processing sheet with id= 62, first strand: chain 'l' and resid 42 through 46 removed outlier: 5.152A pdb=" N LEU l 94 " --> pdb=" O VAL l 111 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 50 through 54 removed outlier: 5.445A pdb=" N LYS l 64 " --> pdb=" O ILE l 80 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE l 80 " --> pdb=" O LYS l 64 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'p' and resid 5 through 11 removed outlier: 3.764A pdb=" N ILE p 20 " --> pdb=" O GLY p 38 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY p 38 " --> pdb=" O ILE p 20 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL p 22 " --> pdb=" O THR p 36 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N THR p 36 " --> pdb=" O VAL p 22 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 8 through 13 removed outlier: 5.556A pdb=" N LYS q 8 " --> pdb=" O GLU q 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL q 61 " --> pdb=" O GLY q 12 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 21 through 32 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 's' and resid 30 through 34 1602 hydrogen bonds defined for protein. 4767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3662 hydrogen bonds 5816 hydrogen bond angles 0 basepair planarities 1460 basepair parallelities 2666 stacking parallelities Total time for adding SS restraints: 211.16 Time building geometry restraints manager: 61.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 17348 1.32 - 1.45: 67098 1.45 - 1.57: 59361 1.57 - 1.70: 9224 1.70 - 1.82: 240 Bond restraints: 153271 Sorted by residual: bond pdb=" C10 TEL A3001 " pdb=" N6 TEL A3001 " ideal model delta sigma weight residual 1.476 1.319 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" CA LEU Q 20 " pdb=" C LEU Q 20 " ideal model delta sigma weight residual 1.523 1.464 0.058 1.41e-02 5.03e+03 1.71e+01 bond pdb=" C26 TEL A3001 " pdb=" C30 TEL A3001 " ideal model delta sigma weight residual 1.573 1.500 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB VAL e 21 " pdb=" CG1 VAL e 21 " ideal model delta sigma weight residual 1.521 1.402 0.119 3.30e-02 9.18e+02 1.29e+01 bond pdb=" C49 TEL A3001 " pdb=" N53 TEL A3001 " ideal model delta sigma weight residual 1.539 1.467 0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 153266 not shown) Histogram of bond angle deviations from ideal: 95.74 - 104.11: 17683 104.11 - 112.49: 91294 112.49 - 120.86: 75997 120.86 - 129.23: 41125 129.23 - 137.60: 3703 Bond angle restraints: 229802 Sorted by residual: angle pdb=" C HIS b 18 " pdb=" N GLN b 19 " pdb=" CA GLN b 19 " ideal model delta sigma weight residual 121.54 137.06 -15.52 1.91e+00 2.74e-01 6.60e+01 angle pdb=" C PRO p 46 " pdb=" N ALA p 47 " pdb=" CA ALA p 47 " ideal model delta sigma weight residual 121.54 134.89 -13.35 1.91e+00 2.74e-01 4.88e+01 angle pdb=" N LYS b 28 " pdb=" CA LYS b 28 " pdb=" C LYS b 28 " ideal model delta sigma weight residual 113.97 105.28 8.69 1.28e+00 6.10e-01 4.61e+01 angle pdb=" C27 TEL A3001 " pdb=" N31 TEL A3001 " pdb=" C36 TEL A3001 " ideal model delta sigma weight residual 145.99 125.65 20.34 3.00e+00 1.11e-01 4.60e+01 angle pdb=" C27 TEL A3001 " pdb=" N31 TEL A3001 " pdb=" C37 TEL A3001 " ideal model delta sigma weight residual 105.37 125.70 -20.33 3.00e+00 1.11e-01 4.59e+01 ... (remaining 229797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 85502 35.98 - 71.96: 11530 71.96 - 107.94: 1222 107.94 - 143.91: 49 143.91 - 179.89: 72 Dihedral angle restraints: 98375 sinusoidal: 83295 harmonic: 15080 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 180.00 110.13 69.87 0 5.00e+00 4.00e-02 1.95e+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 -117.07 -62.93 0 5.00e+00 4.00e-02 1.58e+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 -118.97 -61.03 0 5.00e+00 4.00e-02 1.49e+02 ... (remaining 98372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.082: 29441 1.082 - 2.164: 0 2.164 - 3.245: 0 3.245 - 4.327: 0 4.327 - 5.409: 2 Chirality restraints: 29443 Sorted by residual: chirality pdb=" C28 TEL A3001 " pdb=" C24 TEL A3001 " pdb=" C33 TEL A3001 " pdb=" C34 TEL A3001 " both_signs ideal model delta sigma weight residual False -2.76 2.65 -5.41 2.00e-01 2.50e+01 7.31e+02 chirality pdb=" C21 TEL A3001 " pdb=" C15 TEL A3001 " pdb=" C25 TEL A3001 " pdb=" C26 TEL A3001 " both_signs ideal model delta sigma weight residual False 2.76 -2.59 5.34 2.00e-01 2.50e+01 7.14e+02 chirality pdb=" C3' A A1813 " pdb=" C4' A A1813 " pdb=" O3' A A1813 " pdb=" C2' A A1813 " both_signs ideal model delta sigma weight residual False -2.74 -2.28 -0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 29440 not shown) Planarity restraints: 11883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA d 32 " 0.101 5.00e-02 4.00e+02 1.55e-01 3.84e+01 pdb=" N PRO d 33 " -0.268 5.00e-02 4.00e+02 pdb=" CA PRO d 33 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO d 33 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 50 " -0.094 5.00e-02 4.00e+02 1.42e-01 3.25e+01 pdb=" N PRO R 51 " 0.246 5.00e-02 4.00e+02 pdb=" CA PRO R 51 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO R 51 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS l 57 " 0.072 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO l 58 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO l 58 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO l 58 " 0.059 5.00e-02 4.00e+02 ... (remaining 11880 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 954 2.49 - 3.10: 87585 3.10 - 3.70: 274017 3.70 - 4.30: 407009 4.30 - 4.90: 547544 Nonbonded interactions: 1317109 Sorted by model distance: nonbonded pdb=" NH2 ARG F 80 " pdb=" O6 G x 19 " model vdw 1.892 2.520 nonbonded pdb=" OP2 U A 246 " pdb=" NH2 ARG 3 8 " model vdw 2.072 2.520 nonbonded pdb=" OP2 C a 982 " pdb=" NZ LYS j 59 " model vdw 2.079 2.520 nonbonded pdb=" OP2 G A1846 " pdb=" NH2 ARG C 156 " model vdw 2.080 2.520 nonbonded pdb=" OP2 U A1380 " pdb=" O2' U A1433 " model vdw 2.093 2.440 ... (remaining 1317104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 2.260 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: 0.080 Extract box with map and model: 14.650 Check model and map are aligned: 1.390 Set scattering table: 0.840 Process input model: 480.690 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.310 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 505.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.007 0.157 153271 Z= 0.444 Angle : 1.095 20.338 229802 Z= 0.563 Chirality : 0.071 5.409 29443 Planarity : 0.008 0.155 11883 Dihedral : 24.292 179.892 88668 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.78 % Favored : 90.67 % Rotamer: Outliers : 0.90 % Allowed : 5.13 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.67 % 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: -3.85 (0.09), residues: 5207 helix: -2.77 (0.09), residues: 1645 sheet: -1.83 (0.15), residues: 1015 loop : -2.68 (0.10), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.006 TRP d 9 HIS 0.033 0.004 HIS M 13 PHE 0.047 0.004 PHE p 74 TYR 0.049 0.004 TYR r 28 ARG 0.024 0.002 ARG R 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2159 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 2119 time to evaluate : 5.875 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: F 92 ARG cc_start: 0.6915 (pmm-80) cc_final: 0.6444 (ptp-170) REVERT: F 168 GLU cc_start: 0.6453 (mm-30) cc_final: 0.6253 (mm-30) REVERT: G 72 LEU cc_start: 0.7011 (tt) cc_final: 0.6807 (tt) REVERT: G 110 TYR cc_start: 0.7049 (m-80) cc_final: 0.6792 (m-80) REVERT: K 77 ILE cc_start: 0.7881 (mt) cc_final: 0.6805 (mt) REVERT: O 72 SER cc_start: 0.7261 (p) cc_final: 0.6654 (p) REVERT: W 54 TYR cc_start: 0.7892 (m-80) cc_final: 0.7690 (m-80) REVERT: Y 27 ASN cc_start: 0.7638 (m-40) cc_final: 0.6870 (m-40) REVERT: 1 38 ARG cc_start: 0.6842 (mtp180) cc_final: 0.6520 (mtp180) REVERT: e 127 SER cc_start: 0.8594 (p) cc_final: 0.8305 (p) REVERT: i 129 LYS cc_start: 0.5700 (ttmp) cc_final: 0.4902 (ttpt) REVERT: j 18 LEU cc_start: 0.8323 (tt) cc_final: 0.8034 (tp) REVERT: j 37 SER cc_start: 0.6486 (p) cc_final: 0.6179 (m) REVERT: k 103 GLN cc_start: 0.7376 (mt0) cc_final: 0.7033 (mt0) REVERT: p 18 TYR cc_start: 0.7764 (m-80) cc_final: 0.7542 (m-10) REVERT: p 39 THR cc_start: 0.6755 (p) cc_final: 0.6540 (p) REVERT: r 57 GLN cc_start: 0.7296 (tp-100) cc_final: 0.7050 (tp-100) outliers start: 40 outliers final: 10 residues processed: 2139 average time/residue: 1.3559 time to fit residues: 4811.7878 Evaluate side-chains 1357 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1347 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain k residue 25 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 817 optimal weight: 2.9990 chunk 733 optimal weight: 10.0000 chunk 407 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 494 optimal weight: 2.9990 chunk 391 optimal weight: 5.9990 chunk 758 optimal weight: 1.9990 chunk 293 optimal weight: 20.0000 chunk 461 optimal weight: 2.9990 chunk 564 optimal weight: 1.9990 chunk 879 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN C 142 HIS C 177 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 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 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 10 ASN E 29 ASN E 46 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN G 49 ASN G 66 HIS G 148 ASN J 96 ASN J 118 GLN L 38 GLN M 13 HIS M 44 ASN ** N 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN O 15 HIS P 36 ASN ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Q 38 GLN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 ASN S 102 HIS T 55 ASN U 64 HIS ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 40 HIS ** 0 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 26 ASN 3 35 ASN 3 60 GLN ** 6 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 18 HIS b 24 ASN b 36 ASN b 123 ASN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 136 GLN d 118 HIS e 45 HIS e 83 HIS e 93 ASN f 33 ASN f 66 GLN g 28 ASN g 40 GLN g 56 ASN g 64 GLN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 ASN ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 5 GLN j 64 GLN l 35 HIS l 85 HIS l 109 HIS l 125 GLN n 10 GLN ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 42 HIS o 51 HIS ** o 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 88 GLN q 5 ASN q 49 HIS r 69 GLN t 42 ASN ** t 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 153271 Z= 0.193 Angle : 0.688 26.390 229802 Z= 0.354 Chirality : 0.041 2.001 29443 Planarity : 0.006 0.118 11883 Dihedral : 24.963 179.255 77977 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.61 % Favored : 91.97 % Rotamer: Outliers : 4.44 % Allowed : 15.69 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.60 % 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: -2.55 (0.10), residues: 5207 helix: -0.94 (0.11), residues: 1679 sheet: -1.46 (0.15), residues: 983 loop : -2.30 (0.11), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP c 200 HIS 0.019 0.001 HIS t 68 PHE 0.030 0.002 PHE 6 59 TYR 0.038 0.002 TYR r 28 ARG 0.010 0.001 ARG b 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1665 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1468 time to evaluate : 5.965 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: N 103 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7472 (mtpt) REVERT: S 65 ASP cc_start: 0.5955 (p0) cc_final: 0.5737 (p0) REVERT: Z 46 MET cc_start: 0.7687 (mtt) cc_final: 0.7332 (mtt) REVERT: 0 18 THR cc_start: 0.8090 (m) cc_final: 0.7763 (m) REVERT: 2 14 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7966 (mttp) REVERT: 3 57 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7579 (ttm110) REVERT: 6 43 TYR cc_start: 0.6806 (m-80) cc_final: 0.6605 (m-10) REVERT: c 101 ASN cc_start: 0.6509 (m-40) cc_final: 0.6178 (m-40) REVERT: h 22 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.8092 (m170) REVERT: i 107 ASP cc_start: 0.7762 (p0) cc_final: 0.7455 (p0) REVERT: j 6 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7115 (mt) REVERT: j 19 ASP cc_start: 0.6511 (m-30) cc_final: 0.5874 (m-30) REVERT: k 103 GLN cc_start: 0.7156 (mt0) cc_final: 0.6888 (mt0) REVERT: p 18 TYR cc_start: 0.7614 (m-80) cc_final: 0.7413 (m-10) outliers start: 197 outliers final: 102 residues processed: 1572 average time/residue: 1.2566 time to fit residues: 3379.5404 Evaluate side-chains 1359 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1255 time to evaluate : 5.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 80 PHE Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 119 LYS Chi-restraints excluded: chain b residue 170 ARG Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 128 SER Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 146 ARG Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 46 SER Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 59 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 128 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 108 GLU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain o residue 18 HIS Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain q residue 17 ASP Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain t residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 488 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 731 optimal weight: 10.0000 chunk 598 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 chunk 880 optimal weight: 20.0000 chunk 951 optimal weight: 20.0000 chunk 784 optimal weight: 30.0000 chunk 873 optimal weight: 8.9990 chunk 300 optimal weight: 9.9990 chunk 706 optimal weight: 20.0000 overall best weight: 9.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 HIS C 226 ASN C 230 HIS C 232 HIS C 264 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 9 GLN E 46 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 62 HIS G 107 ASN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 44 ASN ** N 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 ASN ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN U 44 HIS U 58 ASN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 4 ASN 3 35 ASN 4 36 GLN 6 60 ASN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 55 GLN d 82 HIS d 109 GLN e 54 GLN e 93 ASN f 27 ASN f 66 GLN g 28 ASN g 122 ASN i 66 ASN i 126 GLN j 15 HIS l 35 HIS o 13 ASN o 28 GLN o 37 ASN o 46 HIS ** o 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 153271 Z= 0.471 Angle : 0.808 26.254 229802 Z= 0.414 Chirality : 0.048 2.193 29443 Planarity : 0.006 0.117 11883 Dihedral : 24.898 178.114 77974 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.10 % Favored : 90.57 % Rotamer: Outliers : 6.19 % Allowed : 18.28 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.60 % 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: -2.26 (0.11), residues: 5207 helix: -0.49 (0.12), residues: 1703 sheet: -1.48 (0.16), residues: 915 loop : -2.22 (0.11), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP M 65 HIS 0.019 0.002 HIS t 68 PHE 0.023 0.003 PHE 0 5 TYR 0.041 0.003 TYR r 28 ARG 0.012 0.001 ARG Y 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1562 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1287 time to evaluate : 5.918 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: D 140 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7132 (p-80) REVERT: G 39 HIS cc_start: 0.6867 (t-90) cc_final: 0.6479 (t70) REVERT: J 59 ASN cc_start: 0.7857 (m-40) cc_final: 0.7541 (t0) REVERT: J 97 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.5324 (p90) REVERT: L 29 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7442 (tmmm) REVERT: O 46 ASP cc_start: 0.6826 (t0) cc_final: 0.6550 (t70) REVERT: 0 18 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8039 (m) REVERT: b 38 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.5988 (pt) REVERT: b 100 THR cc_start: 0.7328 (p) cc_final: 0.7045 (t) REVERT: g 86 GLN cc_start: 0.7330 (mp10) cc_final: 0.7099 (mp10) REVERT: h 22 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.8072 (m170) REVERT: i 87 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.6908 (tp) REVERT: i 94 TYR cc_start: 0.5734 (OUTLIER) cc_final: 0.3890 (p90) REVERT: i 107 ASP cc_start: 0.8107 (p0) cc_final: 0.7660 (p0) REVERT: j 37 SER cc_start: 0.6751 (p) cc_final: 0.6448 (t) REVERT: k 103 GLN cc_start: 0.7304 (mt0) cc_final: 0.6945 (mt0) REVERT: k 124 ARG cc_start: 0.7685 (ptm-80) cc_final: 0.7475 (ptm-80) REVERT: l 57 LYS cc_start: 0.7260 (tptt) cc_final: 0.7057 (tttp) REVERT: m 52 GLU cc_start: 0.6361 (pt0) cc_final: 0.6125 (pt0) outliers start: 275 outliers final: 186 residues processed: 1443 average time/residue: 1.2637 time to fit residues: 3161.9232 Evaluate side-chains 1378 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1184 time to evaluate : 5.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 70 ASN Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 39 ARG Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 48 GLU Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 80 PHE Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 18 THR Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 170 ARG Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 146 ARG Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 46 SER Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 59 ILE Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 94 TYR Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 40 HIS Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain k residue 108 GLU Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 83 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain m residue 110 LYS Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 36 LYS Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain q residue 17 ASP Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 25 THR Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 43 GLN Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 870 optimal weight: 8.9990 chunk 662 optimal weight: 10.0000 chunk 457 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 420 optimal weight: 2.9990 chunk 591 optimal weight: 10.0000 chunk 883 optimal weight: 9.9990 chunk 935 optimal weight: 7.9990 chunk 461 optimal weight: 4.9990 chunk 837 optimal weight: 0.5980 chunk 252 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN C 264 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN G 107 ASN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN T 58 ASN U 58 ASN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 GLN 1 4 ASN 2 9 ASN 3 35 ASN 6 47 GLN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 55 GLN e 54 GLN g 40 GLN g 56 ASN g 122 ASN l 109 HIS o 28 GLN o 72 ASN r 57 GLN ** r 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 153271 Z= 0.260 Angle : 0.665 27.518 229802 Z= 0.343 Chirality : 0.041 2.160 29443 Planarity : 0.005 0.115 11883 Dihedral : 24.830 178.829 77974 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.16 % Favored : 91.55 % Rotamer: Outliers : 5.99 % Allowed : 20.20 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.60 % 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: -1.85 (0.11), residues: 5207 helix: 0.00 (0.12), residues: 1682 sheet: -1.32 (0.16), residues: 912 loop : -2.05 (0.11), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 65 HIS 0.022 0.001 HIS l 35 PHE 0.019 0.002 PHE M 104 TYR 0.041 0.002 TYR r 28 ARG 0.010 0.001 ARG Y 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1543 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1277 time to evaluate : 5.910 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: C 117 MET cc_start: 0.6386 (mmt) cc_final: 0.6077 (tpt) REVERT: C 247 MET cc_start: 0.7870 (mtt) cc_final: 0.7369 (mtt) REVERT: D 42 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6465 (pm20) REVERT: D 140 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.6981 (p-80) REVERT: G 39 HIS cc_start: 0.6764 (t-90) cc_final: 0.6554 (t70) REVERT: J 59 ASN cc_start: 0.7880 (m-40) cc_final: 0.7536 (t0) REVERT: J 94 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7420 (mtm-85) REVERT: K 5 GLU cc_start: 0.6259 (mm-30) cc_final: 0.5976 (mm-30) REVERT: O 38 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8162 (mttp) REVERT: P 39 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6155 (ppp80) REVERT: W 52 LYS cc_start: 0.7802 (mtpp) cc_final: 0.7533 (mtpp) REVERT: 0 18 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7770 (m) REVERT: 0 41 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7523 (mtt90) REVERT: 4 18 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7259 (ttm-80) REVERT: b 38 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.5853 (pt) REVERT: b 100 THR cc_start: 0.7271 (p) cc_final: 0.7006 (t) REVERT: c 27 ASP cc_start: 0.5300 (t0) cc_final: 0.4697 (t70) REVERT: g 122 ASN cc_start: 0.7001 (m-40) cc_final: 0.6625 (m110) REVERT: h 22 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.8168 (m170) REVERT: i 107 ASP cc_start: 0.8155 (p0) cc_final: 0.7627 (p0) REVERT: k 103 GLN cc_start: 0.7191 (mt0) cc_final: 0.6841 (mt0) REVERT: m 87 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.7002 (ttt90) outliers start: 266 outliers final: 188 residues processed: 1423 average time/residue: 1.2286 time to fit residues: 3027.4667 Evaluate side-chains 1385 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1188 time to evaluate : 5.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain K residue 9 LYS Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 39 ARG Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 LYS Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain 0 residue 18 THR Chi-restraints excluded: chain 0 residue 33 CYS Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 170 ARG Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 146 ARG Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 46 SER Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 59 ILE Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 20 GLN Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 40 HIS Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 87 ARG Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 17 ASP Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 33 HIS Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 43 GLN Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 779 optimal weight: 5.9990 chunk 531 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 696 optimal weight: 10.0000 chunk 386 optimal weight: 5.9990 chunk 798 optimal weight: 10.0000 chunk 646 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 477 optimal weight: 0.1980 chunk 839 optimal weight: 6.9990 chunk 236 optimal weight: 10.0000 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN C 264 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN L 54 GLN ** N 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 4 ASN 3 35 ASN 6 47 GLN b 108 GLN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN d 52 GLN d 55 GLN ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN g 56 ASN l 35 HIS m 76 ASN o 72 ASN r 69 GLN ** t 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 153271 Z= 0.301 Angle : 0.676 27.292 229802 Z= 0.348 Chirality : 0.041 2.156 29443 Planarity : 0.005 0.116 11883 Dihedral : 24.766 179.442 77974 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.06 % Favored : 90.65 % Rotamer: Outliers : 6.67 % Allowed : 20.67 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.71 (0.11), residues: 5207 helix: 0.14 (0.12), residues: 1677 sheet: -1.23 (0.16), residues: 912 loop : -1.98 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 65 HIS 0.030 0.002 HIS l 109 PHE 0.024 0.002 PHE M 104 TYR 0.034 0.002 TYR s 80 ARG 0.011 0.001 ARG Y 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1518 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1222 time to evaluate : 5.976 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: C 247 MET cc_start: 0.7865 (mtt) cc_final: 0.7386 (mtt) REVERT: D 42 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6625 (pm20) REVERT: D 140 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.6941 (p-80) REVERT: G 95 TYR cc_start: 0.5903 (m-80) cc_final: 0.5696 (m-80) REVERT: J 59 ASN cc_start: 0.7899 (m-40) cc_final: 0.7514 (t0) REVERT: J 88 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7194 (mtm-85) REVERT: J 94 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7390 (mtm-85) REVERT: J 97 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.5811 (p90) REVERT: K 81 GLU cc_start: 0.6917 (pt0) cc_final: 0.6627 (pt0) REVERT: N 103 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7862 (mtpt) REVERT: O 1 MET cc_start: 0.6874 (tpp) cc_final: 0.6610 (tpt) REVERT: P 39 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6375 (ppp80) REVERT: W 25 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: 4 18 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.7235 (ttm-80) REVERT: 6 5 ILE cc_start: 0.6837 (mt) cc_final: 0.6630 (mt) REVERT: b 38 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.5955 (pt) REVERT: b 89 MET cc_start: 0.7191 (mmp) cc_final: 0.6844 (mmt) REVERT: b 100 THR cc_start: 0.7345 (p) cc_final: 0.7102 (t) REVERT: d 88 ILE cc_start: 0.8853 (mm) cc_final: 0.8502 (mm) REVERT: i 94 TYR cc_start: 0.5476 (OUTLIER) cc_final: 0.3809 (p90) REVERT: i 107 ASP cc_start: 0.8176 (p0) cc_final: 0.7616 (p0) REVERT: j 37 SER cc_start: 0.6649 (p) cc_final: 0.6361 (t) REVERT: k 103 GLN cc_start: 0.7111 (mt0) cc_final: 0.6755 (mt0) REVERT: m 87 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7008 (ttt90) REVERT: p 55 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7993 (mp) outliers start: 296 outliers final: 225 residues processed: 1391 average time/residue: 1.3470 time to fit residues: 3275.3466 Evaluate side-chains 1388 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1153 time to evaluate : 5.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 91 GLU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 39 ARG Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 LYS Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 175 GLU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 146 ARG Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 21 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain f residue 16 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 46 SER Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 59 ILE Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 94 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 40 HIS Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 83 ILE Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 87 ARG Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 17 ASP Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 33 HIS Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 43 GLN Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 314 optimal weight: 8.9990 chunk 842 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 549 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 chunk 936 optimal weight: 7.9990 chunk 777 optimal weight: 10.0000 chunk 433 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 chunk 491 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 152 ASN D 173 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN J 8 ASN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN T 58 ASN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 4 ASN 2 9 ASN 3 35 ASN 6 47 GLN ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN d 52 GLN d 55 GLN ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 ASN l 35 HIS o 72 ASN s 57 HIS ** t 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 84 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 153271 Z= 0.246 Angle : 0.643 27.599 229802 Z= 0.331 Chirality : 0.039 2.149 29443 Planarity : 0.005 0.116 11883 Dihedral : 24.722 179.704 77972 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.58 % Favored : 91.13 % Rotamer: Outliers : 6.44 % Allowed : 21.44 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.56 (0.11), residues: 5207 helix: 0.30 (0.13), residues: 1675 sheet: -1.15 (0.16), residues: 921 loop : -1.92 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 65 HIS 0.029 0.001 HIS l 35 PHE 0.021 0.002 PHE M 104 TYR 0.030 0.002 TYR r 28 ARG 0.007 0.001 ARG Y 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1510 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1224 time to evaluate : 5.995 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: C 37 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8358 (tp) REVERT: C 247 MET cc_start: 0.7857 (mtt) cc_final: 0.7393 (mtt) REVERT: D 42 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6599 (pm20) REVERT: D 140 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.6927 (p-80) REVERT: G 95 TYR cc_start: 0.5842 (m-80) cc_final: 0.5599 (m-80) REVERT: J 59 ASN cc_start: 0.7858 (m-40) cc_final: 0.7479 (t0) REVERT: J 94 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7359 (mtm-85) REVERT: J 97 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.5908 (p90) REVERT: L 29 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6957 (tmmm) REVERT: P 39 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6310 (ppp80) REVERT: R 16 GLU cc_start: 0.7636 (tp30) cc_final: 0.7350 (tp30) REVERT: W 25 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: Y 14 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7163 (mt) REVERT: 2 22 MET cc_start: 0.7862 (mmm) cc_final: 0.7223 (mmm) REVERT: 6 9 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.5160 (m-80) REVERT: b 18 HIS cc_start: 0.4831 (OUTLIER) cc_final: 0.4606 (t-90) REVERT: b 38 ILE cc_start: 0.6529 (OUTLIER) cc_final: 0.5996 (pt) REVERT: b 100 THR cc_start: 0.7357 (p) cc_final: 0.7113 (t) REVERT: b 106 THR cc_start: 0.8398 (p) cc_final: 0.8094 (p) REVERT: d 88 ILE cc_start: 0.8781 (mm) cc_final: 0.8473 (mm) REVERT: g 122 ASN cc_start: 0.6962 (m-40) cc_final: 0.6743 (m110) REVERT: i 94 TYR cc_start: 0.5470 (OUTLIER) cc_final: 0.4067 (p90) REVERT: i 107 ASP cc_start: 0.8179 (p0) cc_final: 0.7554 (p0) REVERT: k 103 GLN cc_start: 0.7014 (mt0) cc_final: 0.6639 (mt0) REVERT: p 10 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6638 (mtp) REVERT: p 55 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7791 (mp) outliers start: 286 outliers final: 212 residues processed: 1383 average time/residue: 1.2135 time to fit residues: 2903.8735 Evaluate side-chains 1391 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1164 time to evaluate : 5.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 39 ARG Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 LYS Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 33 CYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 175 GLU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 146 ARG Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 14 ARG Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain f residue 16 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 46 SER Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 59 ILE Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 94 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 40 HIS Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 33 HIS Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 902 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 533 optimal weight: 20.0000 chunk 683 optimal weight: 10.0000 chunk 529 optimal weight: 0.9990 chunk 788 optimal weight: 5.9990 chunk 522 optimal weight: 9.9990 chunk 932 optimal weight: 20.0000 chunk 583 optimal weight: 9.9990 chunk 568 optimal weight: 0.8980 chunk 430 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 58 ASN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 35 ASN ** 6 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 GLN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN g 56 ASN j 56 HIS l 35 HIS o 72 ASN ** t 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 153271 Z= 0.231 Angle : 0.635 27.710 229802 Z= 0.326 Chirality : 0.039 2.145 29443 Planarity : 0.005 0.146 11883 Dihedral : 24.671 179.690 77972 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.87 % Favored : 90.86 % Rotamer: Outliers : 6.73 % Allowed : 21.80 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.45 (0.11), residues: 5207 helix: 0.42 (0.13), residues: 1675 sheet: -1.05 (0.16), residues: 934 loop : -1.88 (0.11), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 65 HIS 0.019 0.001 HIS t 68 PHE 0.020 0.002 PHE M 104 TYR 0.025 0.002 TYR r 28 ARG 0.010 0.001 ARG 6 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1209 time to evaluate : 5.863 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: C 37 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8342 (tp) REVERT: C 210 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7679 (ttt90) REVERT: C 247 MET cc_start: 0.7780 (mtt) cc_final: 0.7311 (mtt) REVERT: D 42 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: D 140 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.6965 (p-80) REVERT: E 126 LEU cc_start: 0.7769 (mt) cc_final: 0.7430 (mp) REVERT: G 39 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6740 (t-90) REVERT: J 59 ASN cc_start: 0.7848 (m-40) cc_final: 0.7478 (t0) REVERT: J 76 TYR cc_start: 0.8371 (m-80) cc_final: 0.7984 (m-80) REVERT: J 94 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7343 (mtm-85) REVERT: J 97 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.5878 (p90) REVERT: L 29 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7030 (tmmm) REVERT: N 113 PRO cc_start: 0.7877 (Cg_endo) cc_final: 0.7674 (Cg_exo) REVERT: P 39 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6356 (ppp80) REVERT: Q 48 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7152 (ptt-90) REVERT: R 16 GLU cc_start: 0.7681 (tp30) cc_final: 0.7205 (tp30) REVERT: W 25 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: X 39 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7400 (pp) REVERT: Y 14 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7095 (mt) REVERT: 1 4 ASN cc_start: 0.7787 (m-40) cc_final: 0.7494 (m110) REVERT: 1 5 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7535 (mm) REVERT: 2 22 MET cc_start: 0.7772 (mmm) cc_final: 0.7144 (mmm) REVERT: 6 9 PHE cc_start: 0.6205 (OUTLIER) cc_final: 0.5155 (m-80) REVERT: b 18 HIS cc_start: 0.4713 (OUTLIER) cc_final: 0.4503 (t-90) REVERT: b 38 ILE cc_start: 0.6509 (OUTLIER) cc_final: 0.5993 (pt) REVERT: b 100 THR cc_start: 0.7389 (p) cc_final: 0.7134 (t) REVERT: b 103 ASN cc_start: 0.7543 (t0) cc_final: 0.7287 (t0) REVERT: c 161 ILE cc_start: 0.8392 (mm) cc_final: 0.8186 (tp) REVERT: d 88 ILE cc_start: 0.8748 (mm) cc_final: 0.8458 (mm) REVERT: e 21 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7575 (m) REVERT: h 22 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.8147 (m170) REVERT: h 114 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.7512 (p) REVERT: i 94 TYR cc_start: 0.5459 (OUTLIER) cc_final: 0.4057 (p90) REVERT: i 107 ASP cc_start: 0.8144 (p0) cc_final: 0.7522 (p0) REVERT: j 68 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7395 (mtp180) REVERT: k 103 GLN cc_start: 0.7017 (mt0) cc_final: 0.6669 (mt0) REVERT: l 96 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7688 (ptt90) REVERT: p 10 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6380 (mtp) REVERT: p 55 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7876 (mp) outliers start: 299 outliers final: 223 residues processed: 1379 average time/residue: 1.3026 time to fit residues: 3127.4751 Evaluate side-chains 1403 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1156 time to evaluate : 5.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 28 HIS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 91 GLU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 39 ARG Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 LYS Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 46 CYS Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 156 ASP Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 175 GLU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 146 ARG Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 21 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 16 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 59 ILE Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 94 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 40 HIS Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 34 GLU Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 83 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 96 ARG Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 33 HIS Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain t residue 42 ASN Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 577 optimal weight: 0.2980 chunk 372 optimal weight: 20.0000 chunk 557 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 593 optimal weight: 20.0000 chunk 635 optimal weight: 20.0000 chunk 461 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 733 optimal weight: 20.0000 overall best weight: 5.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN W 37 GLN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 35 ASN 6 20 ASN 6 47 GLN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN g 122 ASN l 5 ASN l 35 HIS m 76 ASN o 72 ASN ** t 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 153271 Z= 0.281 Angle : 0.656 27.256 229802 Z= 0.337 Chirality : 0.040 2.151 29443 Planarity : 0.005 0.138 11883 Dihedral : 24.653 179.772 77972 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.03 % Favored : 90.70 % Rotamer: Outliers : 6.60 % Allowed : 22.52 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.41 (0.11), residues: 5207 helix: 0.42 (0.13), residues: 1672 sheet: -1.00 (0.17), residues: 925 loop : -1.84 (0.11), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 65 HIS 0.018 0.001 HIS t 68 PHE 0.025 0.002 PHE M 104 TYR 0.030 0.002 TYR G 95 ARG 0.007 0.001 ARG G 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1178 time to evaluate : 5.930 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: C 37 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8420 (tp) REVERT: C 210 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7740 (ttt90) REVERT: C 247 MET cc_start: 0.7831 (mtt) cc_final: 0.7399 (mtt) REVERT: D 42 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6652 (pm20) REVERT: D 140 HIS cc_start: 0.8109 (OUTLIER) cc_final: 0.6971 (p-80) REVERT: G 39 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.6776 (t-90) REVERT: J 59 ASN cc_start: 0.7876 (m-40) cc_final: 0.7481 (t0) REVERT: J 76 TYR cc_start: 0.8359 (m-80) cc_final: 0.8010 (m-80) REVERT: J 94 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7374 (mtm-85) REVERT: J 97 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.5977 (p90) REVERT: L 29 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7365 (ttmm) REVERT: P 39 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6425 (ppp80) REVERT: Q 48 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7150 (ptt-90) REVERT: R 16 GLU cc_start: 0.7668 (tp30) cc_final: 0.7208 (tp30) REVERT: W 25 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6899 (tm-30) REVERT: Y 14 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7125 (mt) REVERT: 1 4 ASN cc_start: 0.7695 (m-40) cc_final: 0.7417 (m110) REVERT: 1 5 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7577 (mm) REVERT: 2 22 MET cc_start: 0.7777 (mmm) cc_final: 0.7257 (mmm) REVERT: 6 9 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5037 (m-80) REVERT: b 18 HIS cc_start: 0.4733 (OUTLIER) cc_final: 0.4529 (t-90) REVERT: b 38 ILE cc_start: 0.6579 (OUTLIER) cc_final: 0.6078 (pt) REVERT: b 103 ASN cc_start: 0.7606 (t0) cc_final: 0.7347 (t0) REVERT: c 161 ILE cc_start: 0.8465 (mm) cc_final: 0.8258 (tp) REVERT: d 88 ILE cc_start: 0.8772 (mm) cc_final: 0.8495 (mm) REVERT: h 22 HIS cc_start: 0.8556 (OUTLIER) cc_final: 0.8192 (m170) REVERT: i 94 TYR cc_start: 0.5590 (OUTLIER) cc_final: 0.4156 (p90) REVERT: i 107 ASP cc_start: 0.8172 (p0) cc_final: 0.7537 (p0) REVERT: k 103 GLN cc_start: 0.7029 (mt0) cc_final: 0.6674 (mt0) REVERT: l 96 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7746 (ptt90) REVERT: p 55 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7917 (mp) REVERT: p 71 ARG cc_start: 0.7574 (tmt-80) cc_final: 0.7325 (tmt-80) REVERT: q 59 ASP cc_start: 0.6341 (t0) cc_final: 0.6127 (t0) outliers start: 293 outliers final: 235 residues processed: 1338 average time/residue: 1.2243 time to fit residues: 2831.7627 Evaluate side-chains 1406 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1151 time to evaluate : 5.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 91 GLU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 39 ARG Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 64 MET Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 LYS Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 175 GLU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 146 ARG Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 14 ARG Chi-restraints excluded: chain e residue 21 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain f residue 16 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 59 ILE Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 94 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 40 HIS Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 34 GLU Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 83 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 96 ARG Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 36 LYS Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 33 HIS Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain t residue 42 ASN Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 848 optimal weight: 10.0000 chunk 893 optimal weight: 10.0000 chunk 815 optimal weight: 1.9990 chunk 869 optimal weight: 5.9990 chunk 523 optimal weight: 10.0000 chunk 378 optimal weight: 9.9990 chunk 682 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 785 optimal weight: 6.9990 chunk 822 optimal weight: 9.9990 chunk 866 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN W 37 GLN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 35 ASN 6 20 ASN ** 6 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 HIS ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN g 122 ASN l 5 ASN o 72 ASN ** t 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 153271 Z= 0.356 Angle : 0.707 27.274 229802 Z= 0.363 Chirality : 0.042 2.155 29443 Planarity : 0.005 0.136 11883 Dihedral : 24.678 178.816 77972 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.56 % Favored : 90.19 % Rotamer: Outliers : 6.69 % Allowed : 22.72 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -1.51 (0.11), residues: 5207 helix: 0.27 (0.12), residues: 1685 sheet: -1.08 (0.16), residues: 954 loop : -1.86 (0.11), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 65 HIS 0.021 0.002 HIS l 35 PHE 0.027 0.002 PHE M 104 TYR 0.033 0.002 TYR G 95 ARG 0.015 0.001 ARG i 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1470 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1173 time to evaluate : 5.986 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: C 37 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8417 (tp) REVERT: C 210 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7775 (ttt90) REVERT: C 247 MET cc_start: 0.7944 (mtt) cc_final: 0.7603 (mtt) REVERT: D 42 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6647 (pm20) REVERT: D 140 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7045 (p-80) REVERT: J 59 ASN cc_start: 0.7953 (m-40) cc_final: 0.7562 (t0) REVERT: J 76 TYR cc_start: 0.8392 (m-80) cc_final: 0.8067 (m-80) REVERT: J 94 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7393 (mtm-85) REVERT: J 97 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6114 (p90) REVERT: P 39 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6629 (ppp80) REVERT: Q 48 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7304 (ptt-90) REVERT: W 25 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: Y 14 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7176 (mt) REVERT: 1 4 ASN cc_start: 0.7787 (m-40) cc_final: 0.7546 (m110) REVERT: 6 9 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.4913 (m-80) REVERT: b 18 HIS cc_start: 0.4777 (OUTLIER) cc_final: 0.4508 (t-90) REVERT: b 38 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6144 (pt) REVERT: b 103 ASN cc_start: 0.7625 (t0) cc_final: 0.7360 (t0) REVERT: c 23 TYR cc_start: 0.7516 (t80) cc_final: 0.7173 (t80) REVERT: d 88 ILE cc_start: 0.8848 (mm) cc_final: 0.8500 (mm) REVERT: h 22 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.8192 (m170) REVERT: h 114 THR cc_start: 0.8168 (p) cc_final: 0.7836 (p) REVERT: i 94 TYR cc_start: 0.5850 (OUTLIER) cc_final: 0.4343 (p90) REVERT: i 107 ASP cc_start: 0.8246 (p0) cc_final: 0.7638 (p0) REVERT: k 103 GLN cc_start: 0.7052 (mt0) cc_final: 0.6673 (mt0) REVERT: l 96 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7825 (ptt90) REVERT: p 71 ARG cc_start: 0.7681 (tmt-80) cc_final: 0.7443 (tmt-80) outliers start: 297 outliers final: 241 residues processed: 1340 average time/residue: 1.2228 time to fit residues: 2824.5813 Evaluate side-chains 1394 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1137 time to evaluate : 5.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 28 HIS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 91 GLU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 39 ARG Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 45 LYS Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 24 THR Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 175 GLU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 146 ARG Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 21 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 16 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 46 SER Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 59 ILE Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 94 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 40 HIS Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 31 PHE Chi-restraints excluded: chain l residue 34 GLU Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 83 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 96 ARG Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 36 LYS Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 33 HIS Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 42 ASN Chi-restraints excluded: chain t residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 570 optimal weight: 8.9990 chunk 919 optimal weight: 6.9990 chunk 561 optimal weight: 0.9990 chunk 436 optimal weight: 0.0270 chunk 639 optimal weight: 20.0000 chunk 964 optimal weight: 20.0000 chunk 887 optimal weight: 1.9990 chunk 767 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 593 optimal weight: 20.0000 chunk 470 optimal weight: 2.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 50 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN ** N 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN W 37 GLN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 23 ASN 3 35 ASN 6 20 ASN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN f 33 ASN g 122 ASN l 35 HIS o 72 ASN ** t 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 153271 Z= 0.180 Angle : 0.624 27.985 229802 Z= 0.319 Chirality : 0.037 2.142 29443 Planarity : 0.005 0.131 11883 Dihedral : 24.667 178.017 77972 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.12 % Favored : 91.67 % Rotamer: Outliers : 4.64 % Allowed : 24.77 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.32 (0.11), residues: 5207 helix: 0.46 (0.13), residues: 1669 sheet: -0.88 (0.17), residues: 895 loop : -1.79 (0.11), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP h 132 HIS 0.022 0.001 HIS t 68 PHE 0.021 0.002 PHE b 69 TYR 0.035 0.002 TYR G 95 ARG 0.010 0.001 ARG 6 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10414 Ramachandran restraints generated. 5207 Oldfield, 0 Emsley, 5207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1219 time to evaluate : 5.959 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: C 247 MET cc_start: 0.7678 (mtt) cc_final: 0.7277 (mtt) REVERT: D 42 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6587 (pm20) REVERT: D 140 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.6923 (p-80) REVERT: J 59 ASN cc_start: 0.7789 (m-40) cc_final: 0.7443 (t0) REVERT: J 76 TYR cc_start: 0.8351 (m-80) cc_final: 0.8024 (m-80) REVERT: J 94 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7298 (mtm-85) REVERT: J 97 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6144 (p90) REVERT: N 113 PRO cc_start: 0.7887 (Cg_endo) cc_final: 0.7673 (Cg_exo) REVERT: R 16 GLU cc_start: 0.7495 (tp30) cc_final: 0.7134 (tp30) REVERT: Y 14 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7080 (mt) REVERT: 6 9 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.4691 (m-80) REVERT: b 18 HIS cc_start: 0.4816 (OUTLIER) cc_final: 0.4408 (t-90) REVERT: b 38 ILE cc_start: 0.6529 (OUTLIER) cc_final: 0.6036 (pt) REVERT: b 103 ASN cc_start: 0.7614 (t0) cc_final: 0.7192 (t0) REVERT: b 106 THR cc_start: 0.8281 (p) cc_final: 0.7966 (p) REVERT: d 88 ILE cc_start: 0.8652 (mm) cc_final: 0.8379 (mm) REVERT: e 21 VAL cc_start: 0.7813 (OUTLIER) cc_final: 0.7524 (m) REVERT: i 94 TYR cc_start: 0.5679 (OUTLIER) cc_final: 0.4235 (p90) REVERT: i 107 ASP cc_start: 0.8180 (p0) cc_final: 0.7547 (p0) REVERT: j 6 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.7036 (mt) REVERT: k 103 GLN cc_start: 0.7024 (mt0) cc_final: 0.6686 (mt0) REVERT: l 96 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7751 (ptt90) outliers start: 206 outliers final: 167 residues processed: 1335 average time/residue: 1.2370 time to fit residues: 2849.4641 Evaluate side-chains 1343 residues out of total 4441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1164 time to evaluate : 5.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 45 LYS Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 146 ARG Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 21 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 16 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 59 ILE Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 94 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 40 HIS Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 19 SER Chi-restraints excluded: chain l residue 31 PHE Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 96 ARG Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 11 GLN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 33 HIS Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 609 optimal weight: 20.0000 chunk 818 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 708 optimal weight: 20.0000 chunk 113 optimal weight: 40.0000 chunk 213 optimal weight: 40.0000 chunk 769 optimal weight: 7.9990 chunk 321 optimal weight: 0.8980 chunk 789 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 overall best weight: 6.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 35 ASN ** 3 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 64 ASN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 ASN g 56 ASN g 122 ASN ** k 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 72 ASN ** t 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.085789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.068250 restraints weight = 436431.987| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.27 r_work: 0.3083 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 153271 Z= 0.358 Angle : 0.703 27.165 229802 Z= 0.360 Chirality : 0.042 2.141 29443 Planarity : 0.005 0.133 11883 Dihedral : 24.625 179.390 77972 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.56 % Favored : 90.22 % Rotamer: Outliers : 4.91 % Allowed : 25.02 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.41 (0.11), residues: 5207 helix: 0.34 (0.13), residues: 1674 sheet: -0.99 (0.17), residues: 936 loop : -1.80 (0.11), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 65 HIS 0.017 0.002 HIS t 68 PHE 0.024 0.002 PHE M 104 TYR 0.037 0.002 TYR c 23 ARG 0.010 0.001 ARG 6 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44216.77 seconds wall clock time: 770 minutes 12.52 seconds (46212.52 seconds total)