Starting phenix.real_space_refine on Tue Feb 20 15:06:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syv_25542/02_2024/7syv_25542_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syv_25542/02_2024/7syv_25542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syv_25542/02_2024/7syv_25542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syv_25542/02_2024/7syv_25542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syv_25542/02_2024/7syv_25542_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syv_25542/02_2024/7syv_25542_neut_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2014 5.49 5 Mg 1 5.21 5 S 207 5.16 5 Na 1 4.78 5 C 47576 2.51 5 N 16115 2.21 5 O 21996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 80": "OD1" <-> "OD2" Residue "Z TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 98": "OE1" <-> "OE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "b GLU 46": "OE1" <-> "OE2" Residue "b ASP 94": "OD1" <-> "OD2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D ASP 271": "OD1" <-> "OD2" Residue "d ASP 54": "OD1" <-> "OD2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "G ASP 32": "OD1" <-> "OD2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G ASP 140": "OD1" <-> "OD2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "G TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 149": "OD1" <-> "OD2" Residue "J ASP 105": "OD1" <-> "OD2" Residue "J TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K ASP 104": "OD1" <-> "OD2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "x GLU 678": "OE1" <-> "OE2" Residue "x ASP 783": "OD1" <-> "OD2" Residue "x PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 860": "OE1" <-> "OE2" Residue "x GLU 990": "OE1" <-> "OE2" Residue "x GLU 1000": "OE1" <-> "OE2" Residue "x TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "O ASP 32": "OD1" <-> "OD2" Residue "O ASP 56": "OD1" <-> "OD2" Residue "P ASP 80": "OD1" <-> "OD2" Residue "Q ASP 27": "OD1" <-> "OD2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 97": "OE1" <-> "OE2" Residue "T GLU 7": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T ASP 81": "OD1" <-> "OD2" Residue "W ASP 67": "OD1" <-> "OD2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X ASP 80": "OD1" <-> "OD2" Residue "Y TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 87912 Number of models: 1 Model: "" Number of chains: 42 Chain: "2" Number of atoms: 35864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1680, 35864 Classifications: {'RNA': 1680} Modifications used: {'5*END': 1, 'rna2p_pur': 143, 'rna2p_pyr': 113, 'rna3p_pur': 746, 'rna3p_pyr': 678} Link IDs: {'rna2p': 255, 'rna3p': 1424} Chain breaks: 10 Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "A" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 822 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "i" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 13, 'rna3p': 61} Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "x" Number of atoms: 4965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4965 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 598} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "z" Number of atoms: 5513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 5513 Classifications: {'RNA': 258} Modifications used: {'rna2p_pur': 25, 'rna2p_pyr': 24, 'rna3p_pur': 109, 'rna3p_pyr': 100} Link IDs: {'rna2p': 48, 'rna3p': 209} Chain breaks: 1 Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 997 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 1, ' NA': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 40199 SG CYS b 23 93.886 131.299 134.738 1.00147.06 S ATOM 40220 SG CYS b 26 97.278 132.013 137.602 1.00155.00 S ATOM 40603 SG CYS b 74 95.676 129.425 136.398 1.00147.02 S ATOM 40622 SG CYS b 77 95.714 130.726 138.279 1.00145.08 S ATOM 52062 SG CYS g 121 138.495 110.318 249.630 1.00483.37 S ATOM 52098 SG CYS g 126 137.625 108.711 247.407 1.00486.64 S ATOM 52216 SG CYS g 141 140.282 112.395 247.426 1.00487.88 S ATOM 52235 SG CYS g 144 136.706 109.787 247.193 1.00494.30 S Time building chain proxies: 34.44, per 1000 atoms: 0.39 Number of scatterers: 87912 At special positions: 0 Unit cell: (240.35, 201.4, 269.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 207 16.00 P 2014 15.00 Mg 1 11.99 Na 1 11.00 O 21996 8.00 N 16115 7.00 C 47576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS x 633 " - pdb=" SG CYS x 718 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 33.51 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " Number of angles added : 12 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10444 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 57 sheets defined 28.6% alpha, 14.5% beta 543 base pairs and 1064 stacking pairs defined. Time for finding SS restraints: 33.93 Creating SS restraints... Processing helix chain 'Z' and resid 37 through 48 Processing helix chain 'Z' and resid 79 through 84 Processing helix chain 'Z' and resid 88 through 93 Processing helix chain 'Z' and resid 104 through 116 Processing helix chain 'Z' and resid 120 through 125 removed outlier: 3.641A pdb=" N VAL Z 125 " --> pdb=" O LYS Z 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'a' and resid 52 through 64 Proline residue: a 63 - end of helix Processing helix chain 'a' and resid 70 through 77 Processing helix chain 'a' and resid 81 through 94 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.796A pdb=" N TYR B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 186 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'b' and resid 50 through 54 Processing helix chain 'b' and resid 75 through 80 Processing helix chain 'b' and resid 90 through 92 No H-bonds generated for 'chain 'b' and resid 90 through 92' Processing helix chain 'C' and resid 58 through 61 No H-bonds generated for 'chain 'C' and resid 58 through 61' Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 158 through 172 Processing helix chain 'C' and resid 181 through 189 Processing helix chain 'C' and resid 193 through 202 removed outlier: 3.723A pdb=" N GLN C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'c' and resid 12 through 17 Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 93 through 97 Processing helix chain 'D' and resid 147 through 160 Processing helix chain 'D' and resid 208 through 216 Processing helix chain 'D' and resid 233 through 247 removed outlier: 4.344A pdb=" N THR D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 270 through 276 removed outlier: 4.005A pdb=" N LYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 28 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 115 through 129 Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 16 through 18 No H-bonds generated for 'chain 'e' and resid 16 through 18' Processing helix chain 'e' and resid 33 through 35 No H-bonds generated for 'chain 'e' and resid 33 through 35' Processing helix chain 'e' and resid 40 through 45 Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 58 through 65 removed outlier: 3.510A pdb=" N LYS F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 248 through 262 Processing helix chain 'f' and resid 84 through 88 Processing helix chain 'f' and resid 108 through 115 Processing helix chain 'G' and resid 68 through 76 Processing helix chain 'G' and resid 87 through 104 Processing helix chain 'G' and resid 108 through 119 Processing helix chain 'G' and resid 143 through 161 Processing helix chain 'G' and resid 169 through 180 removed outlier: 4.692A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 202 Processing helix chain 'g' and resid 101 through 104 Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 138 through 144 Processing helix chain 'H' and resid 182 through 235 Processing helix chain 'I' and resid 18 through 32 Processing helix chain 'I' and resid 66 through 74 removed outlier: 5.499A pdb=" N LYS I 70 " --> pdb=" O PRO I 67 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER I 71 " --> pdb=" O GLN I 68 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS I 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 86 removed outlier: 4.124A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 170 through 180 Processing helix chain 'J' and resid 26 through 28 No H-bonds generated for 'chain 'J' and resid 26 through 28' Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 89 through 92 No H-bonds generated for 'chain 'J' and resid 89 through 92' Processing helix chain 'J' and resid 107 through 117 Processing helix chain 'J' and resid 135 through 138 No H-bonds generated for 'chain 'J' and resid 135 through 138' Processing helix chain 'J' and resid 143 through 155 removed outlier: 5.025A pdb=" N ASN J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 168 Processing helix chain 'J' and resid 192 through 206 removed outlier: 3.506A pdb=" N GLU J 196 " --> pdb=" O LYS J 193 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG J 205 " --> pdb=" O ILE J 202 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS J 206 " --> pdb=" O LYS J 203 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 24 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 40 through 62 Processing helix chain 'K' and resid 68 through 84 Processing helix chain 'K' and resid 94 through 99 removed outlier: 3.643A pdb=" N ILE K 97 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU K 98 " --> pdb=" O ASP K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 removed outlier: 3.950A pdb=" N ARG K 108 " --> pdb=" O ASP K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 117 Processing helix chain 'K' and resid 123 through 131 Processing helix chain 'K' and resid 172 through 185 Processing helix chain 'x' and resid 604 through 619 Processing helix chain 'x' and resid 642 through 650 Processing helix chain 'x' and resid 673 through 678 Processing helix chain 'x' and resid 689 through 692 No H-bonds generated for 'chain 'x' and resid 689 through 692' Processing helix chain 'x' and resid 733 through 744 Processing helix chain 'x' and resid 756 through 758 No H-bonds generated for 'chain 'x' and resid 756 through 758' Processing helix chain 'x' and resid 770 through 776 removed outlier: 3.874A pdb=" N LEU x 774 " --> pdb=" O VAL x 770 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS x 775 " --> pdb=" O ALA x 771 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS x 776 " --> pdb=" O ALA x 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 770 through 776' Processing helix chain 'x' and resid 779 through 799 removed outlier: 3.808A pdb=" N ASP x 783 " --> pdb=" O LYS x 779 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU x 784 " --> pdb=" O ASN x 780 " (cutoff:3.500A) Processing helix chain 'x' and resid 829 through 843 removed outlier: 3.816A pdb=" N LEU x 836 " --> pdb=" O LEU x 832 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL x 837 " --> pdb=" O ILE x 833 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU x 838 " --> pdb=" O TYR x 834 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU x 839 " --> pdb=" O LEU x 835 " (cutoff:3.500A) Processing helix chain 'x' and resid 959 through 966 Processing helix chain 'x' and resid 986 through 998 removed outlier: 3.673A pdb=" N THR x 998 " --> pdb=" O GLU x 994 " (cutoff:3.500A) Processing helix chain 'x' and resid 1013 through 1023 removed outlier: 4.485A pdb=" N MET x1022 " --> pdb=" O LYS x1018 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU x1023 " --> pdb=" O ALA x1019 " (cutoff:3.500A) Processing helix chain 'x' and resid 1027 through 1029 No H-bonds generated for 'chain 'x' and resid 1027 through 1029' Processing helix chain 'x' and resid 1041 through 1050 removed outlier: 4.020A pdb=" N ASP x1048 " --> pdb=" O GLN x1044 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER x1049 " --> pdb=" O GLU x1045 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU x1050 " --> pdb=" O MET x1046 " (cutoff:3.500A) Processing helix chain 'x' and resid 1060 through 1081 Processing helix chain 'x' and resid 1186 through 1194 Processing helix chain 'x' and resid 1202 through 1214 Processing helix chain 'L' and resid 5 through 17 removed outlier: 3.739A pdb=" N ILE L 9 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 55 Processing helix chain 'L' and resid 73 through 83 Processing helix chain 'L' and resid 92 through 94 No H-bonds generated for 'chain 'L' and resid 92 through 94' Processing helix chain 'M' and resid 48 through 52 Processing helix chain 'N' and resid 15 through 27 Processing helix chain 'N' and resid 36 through 43 Processing helix chain 'N' and resid 61 through 69 Processing helix chain 'N' and resid 82 through 89 Processing helix chain 'N' and resid 121 through 129 Processing helix chain 'O' and resid 31 through 43 Processing helix chain 'O' and resid 47 through 57 Processing helix chain 'O' and resid 63 through 66 No H-bonds generated for 'chain 'O' and resid 63 through 66' Processing helix chain 'O' and resid 71 through 78 Processing helix chain 'O' and resid 86 through 102 Processing helix chain 'O' and resid 110 through 131 Processing helix chain 'P' and resid 66 through 68 No H-bonds generated for 'chain 'P' and resid 66 through 68' Processing helix chain 'P' and resid 71 through 88 Processing helix chain 'P' and resid 111 through 121 Processing helix chain 'Q' and resid 22 through 26 Processing helix chain 'Q' and resid 30 through 36 Processing helix chain 'Q' and resid 39 through 45 Processing helix chain 'Q' and resid 55 through 65 Processing helix chain 'Q' and resid 87 through 89 No H-bonds generated for 'chain 'Q' and resid 87 through 89' Processing helix chain 'Q' and resid 109 through 111 No H-bonds generated for 'chain 'Q' and resid 109 through 111' Processing helix chain 'R' and resid 39 through 41 No H-bonds generated for 'chain 'R' and resid 39 through 41' Processing helix chain 'R' and resid 45 through 58 removed outlier: 3.529A pdb=" N GLN R 48 " --> pdb=" O ARG R 45 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR R 49 " --> pdb=" O THR R 46 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU R 53 " --> pdb=" O LYS R 50 " (cutoff:3.500A) Proline residue: R 54 - end of helix removed outlier: 3.694A pdb=" N LEU R 58 " --> pdb=" O VAL R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 63 Processing helix chain 'R' and resid 77 through 98 removed outlier: 3.963A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 115 removed outlier: 4.360A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 119 No H-bonds generated for 'chain 'R' and resid 117 through 119' Processing helix chain 'S' and resid 7 through 19 Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.516A pdb=" N ARG S 33 " --> pdb=" O HIS S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 63 Processing helix chain 'S' and resid 76 through 83 removed outlier: 4.687A pdb=" N ARG S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 107 Processing helix chain 'T' and resid 26 through 32 removed outlier: 4.034A pdb=" N ILE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THR T 31 " --> pdb=" O ALA T 27 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA T 32 " --> pdb=" O PHE T 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 26 through 32' Processing helix chain 'T' and resid 38 through 47 removed outlier: 3.525A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG T 46 " --> pdb=" O HIS T 42 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS T 47 " --> pdb=" O VAL T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 61 through 72 Processing helix chain 'T' and resid 74 through 76 No H-bonds generated for 'chain 'T' and resid 74 through 76' Processing helix chain 'T' and resid 100 through 117 Processing helix chain 'T' and resid 120 through 127 Processing helix chain 'U' and resid 11 through 25 removed outlier: 4.017A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 36 removed outlier: 4.236A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR U 36 " --> pdb=" O TRP U 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 32 through 36' Processing helix chain 'U' and resid 52 through 66 Processing helix chain 'U' and resid 72 through 78 removed outlier: 3.571A pdb=" N THR U 76 " --> pdb=" O VAL U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 109 Processing helix chain 'U' and resid 125 through 142 Processing helix chain 'V' and resid 29 through 45 Processing helix chain 'V' and resid 95 through 103 Processing helix chain 'W' and resid 57 through 62 Processing helix chain 'W' and resid 66 through 76 Processing helix chain 'X' and resid 6 through 19 Processing helix chain 'X' and resid 32 through 43 Processing helix chain 'X' and resid 86 through 93 removed outlier: 3.894A pdb=" N ASN X 92 " --> pdb=" O LYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 119 removed outlier: 3.681A pdb=" N ARG X 118 " --> pdb=" O GLU X 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 22 Processing helix chain 'Y' and resid 26 through 30 Processing helix chain 'Y' and resid 33 through 38 Processing helix chain 'Y' and resid 130 through 135 Processing sheet with id= A, first strand: chain 'Z' and resid 6 through 10 removed outlier: 3.579A pdb=" N THR Z 6 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'Z' and resid 13 through 15 removed outlier: 3.537A pdb=" N ARG Z 20 " --> pdb=" O ASN Z 15 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.857A pdb=" N ILE A 76 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 93 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLY A 80 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL A 91 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ALA A 89 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU A 58 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 91 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N HIS A 60 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LEU A 93 " --> pdb=" O HIS A 60 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 57 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'a' and resid 97 through 101 removed outlier: 3.524A pdb=" N VAL a 100 " --> pdb=" O ILE a 108 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.532A pdb=" N LEU B 121 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE B 77 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 123 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL B 124 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 145 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 159 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS B 148 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE B 161 " --> pdb=" O CYS B 148 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'b' and resid 20 through 22 Processing sheet with id= G, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.511A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.608A pdb=" N GLY C 102 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 124 through 128 removed outlier: 3.559A pdb=" N VAL C 127 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 134 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C 219 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG C 136 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N MET C 217 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N PHE C 138 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C 215 " --> pdb=" O PHE C 138 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 140 through 143 removed outlier: 3.988A pdb=" N PHE C 211 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP C 209 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'c' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'D' and resid 138 through 144 removed outlier: 3.540A pdb=" N VAL D 128 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 142 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.762A pdb=" N VAL D 184 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 193 " --> pdb=" O GLY D 186 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'd' and resid 55 through 58 removed outlier: 3.543A pdb=" N LEU d 58 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS d 10 " --> pdb=" O LEU d 58 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL d 30 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG d 44 " --> pdb=" O VAL d 30 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.730A pdb=" N TYR E 87 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE E 50 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY E 36 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 147 through 155 removed outlier: 3.597A pdb=" N GLY E 140 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS E 141 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL E 181 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 70 through 72 removed outlier: 3.655A pdb=" N GLU F 97 " --> pdb=" O ILE F 92 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 121 through 125 removed outlier: 6.280A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.514A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 225 through 227 removed outlier: 6.949A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 123 through 127 Processing sheet with id= V, first strand: chain 'H' and resid 13 through 16 removed outlier: 3.696A pdb=" N ILE H 113 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL H 108 " --> pdb=" O ASN H 56 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY H 54 " --> pdb=" O ASN H 110 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL H 112 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE H 52 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 72 through 78 Processing sheet with id= X, first strand: chain 'H' and resid 159 through 162 removed outlier: 3.549A pdb=" N LYS H 172 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU H 162 " --> pdb=" O ARG H 170 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG H 170 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'h' and resid 53 through 55 removed outlier: 3.776A pdb=" N SER h 33 " --> pdb=" O ILE h 41 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'h' and resid 66 through 71 removed outlier: 6.742A pdb=" N GLY h 81 " --> pdb=" O SER h 67 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL h 69 " --> pdb=" O LEU h 79 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU h 79 " --> pdb=" O VAL h 69 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ILE h 71 " --> pdb=" O PHE h 77 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE h 77 " --> pdb=" O ILE h 71 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG h 99 " --> pdb=" O LEU h 89 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP h 91 " --> pdb=" O THR h 97 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR h 97 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'h' and resid 108 through 113 removed outlier: 6.658A pdb=" N GLY h 123 " --> pdb=" O LEU h 109 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL h 111 " --> pdb=" O VAL h 121 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL h 121 " --> pdb=" O VAL h 111 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE h 113 " --> pdb=" O GLN h 119 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN h 119 " --> pdb=" O PHE h 113 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER h 122 " --> pdb=" O LYS h 130 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR h 140 " --> pdb=" O LEU h 131 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN h 133 " --> pdb=" O CYS h 138 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS h 138 " --> pdb=" O ASN h 133 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'h' and resid 151 through 156 removed outlier: 6.813A pdb=" N CYS h 168 " --> pdb=" O SER h 152 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL h 154 " --> pdb=" O VAL h 166 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL h 166 " --> pdb=" O VAL h 154 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE h 156 " --> pdb=" O ILE h 164 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE h 164 " --> pdb=" O PHE h 156 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY h 169 " --> pdb=" O LEU h 173 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU h 173 " --> pdb=" O GLY h 169 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR h 186 " --> pdb=" O VAL h 176 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'h' and resid 217 through 220 removed outlier: 3.705A pdb=" N GLY h 210 " --> pdb=" O THR h 197 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR h 197 " --> pdb=" O GLY h 210 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'h' and resid 247 through 251 removed outlier: 4.254A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP h 259 " --> pdb=" O LEU h 248 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE h 258 " --> pdb=" O ASP h 268 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'h' and resid 297 through 301 removed outlier: 3.784A pdb=" N ALA h 300 " --> pdb=" O ARG h 308 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG h 308 " --> pdb=" O ALA h 300 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN h 311 " --> pdb=" O LEU h 7 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU h 7 " --> pdb=" O GLN h 311 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 48 through 51 removed outlier: 3.666A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 184 through 188 removed outlier: 4.575A pdb=" N ASP I 184 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.648A pdb=" N VAL J 46 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS J 54 " --> pdb=" O VAL J 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'J' and resid 72 through 77 removed outlier: 3.634A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY J 187 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.515A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'x' and resid 817 through 820 removed outlier: 4.721A pdb=" N SER x 817 " --> pdb=" O PHE x 749 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA x 721 " --> pdb=" O ILE x 750 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA x 752 " --> pdb=" O ALA x 721 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU x 723 " --> pdb=" O ALA x 752 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN x 754 " --> pdb=" O LEU x 723 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL x 725 " --> pdb=" O ASN x 754 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU x 697 " --> pdb=" O ILE x 632 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL x 634 " --> pdb=" O LEU x 697 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE x 699 " --> pdb=" O VAL x 634 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N GLY x 636 " --> pdb=" O ILE x 699 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'x' and resid 893 through 898 removed outlier: 3.933A pdb=" N GLY x 893 " --> pdb=" O GLY x 890 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR x 885 " --> pdb=" O ALA x 948 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'x' and resid 929 through 932 removed outlier: 4.053A pdb=" N LEU x 932 " --> pdb=" O GLY x 901 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY x 901 " --> pdb=" O LEU x 932 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'x' and resid 980 through 983 removed outlier: 3.556A pdb=" N PHE x1035 " --> pdb=" O GLN x 982 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'x' and resid 1091 through 1093 removed outlier: 3.838A pdb=" N VAL x1181 " --> pdb=" O CYS x1124 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY x1134 " --> pdb=" O MET x1123 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL x1125 " --> pdb=" O ASP x1132 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP x1132 " --> pdb=" O VAL x1125 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS x1158 " --> pdb=" O THR x1137 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE x1139 " --> pdb=" O CYS x1156 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS x1156 " --> pdb=" O ILE x1139 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL x1157 " --> pdb=" O MET x1108 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET x1108 " --> pdb=" O VAL x1157 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU x1113 " --> pdb=" O LYS x1091 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS x1091 " --> pdb=" O GLU x1113 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'x' and resid 858 through 864 removed outlier: 3.711A pdb=" N MET x 859 " --> pdb=" O ASP x 872 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASP x 872 " --> pdb=" O MET x 859 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL x 861 " --> pdb=" O THR x 870 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR x 870 " --> pdb=" O VAL x 861 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA x 863 " --> pdb=" O GLY x 868 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY x 868 " --> pdb=" O ALA x 863 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'L' and resid 58 through 62 removed outlier: 3.766A pdb=" N LYS L 59 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN L 61 " --> pdb=" O TYR L 68 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR L 68 " --> pdb=" O GLN L 61 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'M' and resid 102 through 112 removed outlier: 3.685A pdb=" N MET M 109 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ARG M 89 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL M 77 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASP M 91 " --> pdb=" O GLY M 75 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY M 75 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 15.357A pdb=" N LEU M 93 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 16.299A pdb=" N LEU M 73 " --> pdb=" O LEU M 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS M 144 " --> pdb=" O THR M 127 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'N' and resid 49 through 51 removed outlier: 3.835A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL N 109 " --> pdb=" O VAL N 51 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'P' and resid 52 through 57 removed outlier: 7.425A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA P 92 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N CYS P 31 " --> pdb=" O ALA P 92 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N HIS P 94 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE P 33 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS P 96 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA P 35 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG P 98 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU P 130 " --> pdb=" O ILE P 95 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 75 through 78 removed outlier: 7.079A pdb=" N MET Q 93 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR Q 78 " --> pdb=" O MET Q 93 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY Q 95 " --> pdb=" O THR Q 78 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.622A pdb=" N VAL R 10 " --> pdb=" O CYS R 25 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG R 71 " --> pdb=" O VAL R 22 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP R 67 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL R 70 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'T' and resid 12 through 14 Processing sheet with id= AX, first strand: chain 'U' and resid 81 through 83 removed outlier: 3.537A pdb=" N GLY U 81 " --> pdb=" O SER U 93 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER U 93 " --> pdb=" O GLY U 81 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'U' and resid 113 through 115 Processing sheet with id= AZ, first strand: chain 'V' and resid 85 through 91 removed outlier: 3.524A pdb=" N HIS V 85 " --> pdb=" O SER V 26 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG V 21 " --> pdb=" O THR V 115 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'V' and resid 63 through 66 removed outlier: 3.630A pdb=" N ILE V 63 " --> pdb=" O PHE V 80 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'W' and resid 32 through 37 removed outlier: 3.604A pdb=" N ILE W 32 " --> pdb=" O ILE W 55 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE W 55 " --> pdb=" O ILE W 32 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL W 36 " --> pdb=" O LYS W 51 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'X' and resid 50 through 53 Processing sheet with id= BD, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.578A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS X 124 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET X 111 " --> pdb=" O LEU X 104 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'Y' and resid 80 through 84 removed outlier: 3.525A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA Y 103 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL Y 122 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) 1311 hydrogen bonds defined for protein. 3798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1372 hydrogen bonds 2316 hydrogen bond angles 0 basepair planarities 543 basepair parallelities 1064 stacking parallelities Total time for adding SS restraints: 65.99 Time building geometry restraints manager: 36.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12368 1.33 - 1.45: 35627 1.45 - 1.58: 41412 1.58 - 1.70: 4016 1.70 - 1.82: 320 Bond restraints: 93743 Sorted by residual: bond pdb=" O3' U z 336 " pdb=" P G z 337 " ideal model delta sigma weight residual 1.607 1.724 -0.117 1.50e-02 4.44e+03 6.07e+01 bond pdb=" C1' G z 346 " pdb=" N9 G z 346 " ideal model delta sigma weight residual 1.475 1.367 0.108 1.50e-02 4.44e+03 5.16e+01 bond pdb=" O5' U z 336 " pdb=" C5' U z 336 " ideal model delta sigma weight residual 1.424 1.504 -0.080 1.50e-02 4.44e+03 2.83e+01 bond pdb=" C1' C z 347 " pdb=" N1 C z 347 " ideal model delta sigma weight residual 1.480 1.548 -0.068 1.50e-02 4.44e+03 2.05e+01 bond pdb=" C3' U z 336 " pdb=" O3' U z 336 " ideal model delta sigma weight residual 1.427 1.472 -0.045 1.50e-02 4.44e+03 9.09e+00 ... (remaining 93738 not shown) Histogram of bond angle deviations from ideal: 95.22 - 103.44: 4539 103.44 - 111.66: 50502 111.66 - 119.87: 41803 119.87 - 128.09: 36048 128.09 - 136.30: 3327 Bond angle restraints: 136219 Sorted by residual: angle pdb=" CA PRO Y 141 " pdb=" N PRO Y 141 " pdb=" CD PRO Y 141 " ideal model delta sigma weight residual 112.00 103.12 8.88 1.40e+00 5.10e-01 4.02e+01 angle pdb=" O3' U z 336 " pdb=" C3' U z 336 " pdb=" C2' U z 336 " ideal model delta sigma weight residual 109.50 99.99 9.51 1.50e+00 4.44e-01 4.02e+01 angle pdb=" N GLN H 197 " pdb=" CA GLN H 197 " pdb=" CB GLN H 197 " ideal model delta sigma weight residual 110.40 119.94 -9.54 1.63e+00 3.76e-01 3.42e+01 angle pdb=" C4' U z 336 " pdb=" C3' U z 336 " pdb=" O3' U z 336 " ideal model delta sigma weight residual 109.40 118.06 -8.66 1.50e+00 4.44e-01 3.34e+01 angle pdb=" N GLU x 964 " pdb=" CA GLU x 964 " pdb=" CB GLU x 964 " ideal model delta sigma weight residual 110.40 119.69 -9.29 1.63e+00 3.76e-01 3.25e+01 ... (remaining 136214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 54163 35.95 - 71.91: 4982 71.91 - 107.86: 622 107.86 - 143.81: 10 143.81 - 179.76: 25 Dihedral angle restraints: 59802 sinusoidal: 43619 harmonic: 16183 Sorted by residual: dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 32.33 167.67 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 7.29 -167.29 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' U 21624 " pdb=" C1' U 21624 " pdb=" N1 U 21624 " pdb=" C2 U 21624 " ideal model delta sinusoidal sigma weight residual -160.00 -3.88 -156.12 1 1.50e+01 4.44e-03 8.17e+01 ... (remaining 59799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 15532 0.076 - 0.151: 1205 0.151 - 0.227: 114 0.227 - 0.302: 17 0.302 - 0.378: 6 Chirality restraints: 16874 Sorted by residual: chirality pdb=" C3' A 21825 " pdb=" C4' A 21825 " pdb=" O3' A 21825 " pdb=" C2' A 21825 " both_signs ideal model delta sigma weight residual False -2.48 -2.86 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" P G z 344 " pdb=" OP1 G z 344 " pdb=" OP2 G z 344 " pdb=" O5' G z 344 " both_signs ideal model delta sigma weight residual True 2.41 -2.75 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C1' GTP x1301 " pdb=" C2' GTP x1301 " pdb=" N9 GTP x1301 " pdb=" O4' GTP x1301 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 16871 not shown) Planarity restraints: 9815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG Y 140 " -0.100 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO Y 141 " 0.253 5.00e-02 4.00e+02 pdb=" CA PRO Y 141 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO Y 141 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C 21753 " 0.058 2.00e-02 2.50e+03 3.31e-02 2.46e+01 pdb=" N1 C 21753 " -0.062 2.00e-02 2.50e+03 pdb=" C2 C 21753 " 0.032 2.00e-02 2.50e+03 pdb=" O2 C 21753 " -0.032 2.00e-02 2.50e+03 pdb=" N3 C 21753 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C 21753 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C 21753 " 0.019 2.00e-02 2.50e+03 pdb=" C5 C 21753 " -0.011 2.00e-02 2.50e+03 pdb=" C6 C 21753 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 962 " 0.044 2.00e-02 2.50e+03 2.04e-02 1.15e+01 pdb=" N9 A 2 962 " -0.048 2.00e-02 2.50e+03 pdb=" C8 A 2 962 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A 2 962 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A 2 962 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A 2 962 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A 2 962 " 0.013 2.00e-02 2.50e+03 pdb=" N1 A 2 962 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 2 962 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A 2 962 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A 2 962 " -0.007 2.00e-02 2.50e+03 ... (remaining 9812 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 1552 2.62 - 3.19: 65209 3.19 - 3.76: 160218 3.76 - 4.33: 206347 4.33 - 4.90: 299266 Nonbonded interactions: 732592 Sorted by model distance: nonbonded pdb=" O1G GTP x1301 " pdb="MG MG x1302 " model vdw 2.046 2.170 nonbonded pdb=" O2B GTP x1301 " pdb="MG MG x1302 " model vdw 2.056 2.170 nonbonded pdb=" O2' A 2 561 " pdb=" OE1 GLN K 132 " model vdw 2.184 2.440 nonbonded pdb=" OG SER Q 29 " pdb=" OE1 GLN Q 32 " model vdw 2.265 2.440 nonbonded pdb=" O2' G 21121 " pdb=" O ILE C 204 " model vdw 2.273 2.440 ... (remaining 732587 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 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: 0.050 Extract box with map and model: 16.810 Check model and map are aligned: 1.020 Set scattering table: 0.630 Process input model: 245.670 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.220 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: 0.010 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 272.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 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 : 0.003 0.117 93743 Z= 0.212 Angle : 0.788 14.808 136219 Z= 0.385 Chirality : 0.041 0.378 16874 Planarity : 0.005 0.147 9815 Dihedral : 21.990 179.763 49355 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.06 % Allowed : 0.56 % Favored : 99.38 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.32 (0.10), residues: 5551 helix: -1.56 (0.10), residues: 1699 sheet: -0.71 (0.17), residues: 878 loop : -1.78 (0.10), residues: 2974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP h 17 HIS 0.019 0.001 HIS x 963 PHE 0.037 0.002 PHE X 37 TYR 0.040 0.001 TYR G 188 ARG 0.019 0.000 ARG n 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1476 time to evaluate : 5.147 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: Z 74 MET cc_start: 0.7299 (ptp) cc_final: 0.6898 (ptp) REVERT: Z 81 TYR cc_start: 0.8213 (m-80) cc_final: 0.8008 (m-10) REVERT: Z 110 ARG cc_start: 0.7101 (mtp85) cc_final: 0.6894 (ttt90) REVERT: A 42 LEU cc_start: 0.4816 (mt) cc_final: 0.4486 (mt) REVERT: A 46 ARG cc_start: 0.4827 (mtm180) cc_final: 0.4409 (ptp-170) REVERT: a 52 LYS cc_start: 0.7095 (tptp) cc_final: 0.6661 (ptmm) REVERT: a 66 LYS cc_start: 0.6562 (tttm) cc_final: 0.6087 (tptp) REVERT: a 78 LYS cc_start: 0.6597 (mttp) cc_final: 0.6231 (mmtm) REVERT: a 112 ASN cc_start: 0.5849 (m-40) cc_final: 0.5192 (p0) REVERT: B 14 ASP cc_start: 0.7465 (m-30) cc_final: 0.7135 (p0) REVERT: B 29 ASN cc_start: 0.6479 (m-40) cc_final: 0.6171 (m-40) REVERT: B 80 ARG cc_start: 0.6817 (mmm-85) cc_final: 0.6175 (tpp-160) REVERT: B 112 ILE cc_start: 0.7968 (pt) cc_final: 0.7767 (pt) REVERT: B 136 GLU cc_start: 0.7729 (tp30) cc_final: 0.7162 (tp30) REVERT: b 19 GLN cc_start: 0.7245 (tp-100) cc_final: 0.6863 (tt0) REVERT: b 88 SER cc_start: 0.7252 (p) cc_final: 0.6617 (t) REVERT: b 89 ARG cc_start: 0.6362 (mtp180) cc_final: 0.6144 (tpt170) REVERT: C 29 ASP cc_start: 0.6615 (m-30) cc_final: 0.5762 (m-30) REVERT: C 30 TRP cc_start: 0.7180 (m100) cc_final: 0.6843 (m100) REVERT: C 34 LYS cc_start: 0.5752 (mmtt) cc_final: 0.5480 (mmmt) REVERT: C 39 PHE cc_start: 0.7074 (m-80) cc_final: 0.6736 (m-10) REVERT: C 40 ASN cc_start: 0.7608 (t0) cc_final: 0.7047 (t0) REVERT: C 120 MET cc_start: 0.8627 (ttt) cc_final: 0.7798 (ttt) REVERT: C 202 GLN cc_start: 0.6832 (tp-100) cc_final: 0.6405 (mm110) REVERT: C 213 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7437 (ttp80) REVERT: C 229 MET cc_start: 0.6095 (mmp) cc_final: 0.5041 (ptm) REVERT: c 15 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7096 (mm-30) REVERT: c 16 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7469 (pttp) REVERT: c 22 LYS cc_start: 0.7689 (mttt) cc_final: 0.7481 (mttt) REVERT: c 79 PHE cc_start: 0.7092 (p90) cc_final: 0.6803 (p90) REVERT: D 65 LYS cc_start: 0.6999 (ttpt) cc_final: 0.6689 (ttmt) REVERT: D 68 ARG cc_start: 0.5725 (tpm170) cc_final: 0.5403 (tpp-160) REVERT: D 72 ASP cc_start: 0.5586 (m-30) cc_final: 0.5223 (m-30) REVERT: D 88 ILE cc_start: 0.6633 (mt) cc_final: 0.6324 (mt) REVERT: D 108 LYS cc_start: 0.6412 (tttt) cc_final: 0.5925 (ttpp) REVERT: D 125 LYS cc_start: 0.7508 (ttpt) cc_final: 0.6952 (tttt) REVERT: D 133 TYR cc_start: 0.7930 (m-80) cc_final: 0.7651 (m-80) REVERT: D 176 LYS cc_start: 0.7799 (mtpp) cc_final: 0.7404 (mmtt) REVERT: D 223 TYR cc_start: 0.7479 (m-80) cc_final: 0.7258 (m-80) REVERT: D 230 THR cc_start: 0.6339 (m) cc_final: 0.6100 (p) REVERT: D 241 PHE cc_start: 0.7910 (t80) cc_final: 0.7662 (t80) REVERT: d 10 LYS cc_start: 0.7138 (tttm) cc_final: 0.6517 (mttm) REVERT: E 17 PHE cc_start: 0.6386 (t80) cc_final: 0.5938 (t80) REVERT: E 34 TYR cc_start: 0.5896 (t80) cc_final: 0.5468 (t80) REVERT: E 40 ARG cc_start: 0.5718 (ttt180) cc_final: 0.4852 (mmt180) REVERT: E 66 ILE cc_start: 0.6415 (tp) cc_final: 0.6073 (tt) REVERT: E 72 VAL cc_start: 0.7202 (t) cc_final: 0.6780 (t) REVERT: E 117 ARG cc_start: 0.5733 (mmm160) cc_final: 0.4907 (mmt180) REVERT: E 124 ARG cc_start: 0.5626 (ttm-80) cc_final: 0.5305 (tpm170) REVERT: E 135 GLU cc_start: 0.6458 (tp30) cc_final: 0.6062 (tp30) REVERT: E 136 VAL cc_start: 0.7968 (m) cc_final: 0.7560 (m) REVERT: E 152 PHE cc_start: 0.7022 (m-80) cc_final: 0.6510 (m-80) REVERT: E 157 MET cc_start: 0.6866 (tpp) cc_final: 0.6360 (ptp) REVERT: E 169 ASP cc_start: 0.7029 (m-30) cc_final: 0.6765 (m-30) REVERT: E 187 LYS cc_start: 0.6049 (mtmm) cc_final: 0.5417 (tttm) REVERT: E 190 LEU cc_start: 0.7487 (mm) cc_final: 0.7197 (mt) REVERT: F 54 TYR cc_start: 0.7980 (m-10) cc_final: 0.7124 (m-10) REVERT: F 62 LYS cc_start: 0.6907 (tptt) cc_final: 0.6321 (tptt) REVERT: F 66 MET cc_start: 0.4439 (ptt) cc_final: 0.2814 (ppp) REVERT: F 91 SER cc_start: 0.7100 (m) cc_final: 0.6846 (m) REVERT: F 153 LEU cc_start: 0.7716 (mt) cc_final: 0.7484 (mt) REVERT: F 240 ARG cc_start: 0.6467 (mmm-85) cc_final: 0.6182 (mmt180) REVERT: f 129 ASN cc_start: 0.6363 (t0) cc_final: 0.6103 (t0) REVERT: G 28 VAL cc_start: 0.5847 (m) cc_final: 0.5199 (m) REVERT: G 33 ILE cc_start: 0.8085 (tp) cc_final: 0.7493 (tp) REVERT: G 42 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7318 (tptt) REVERT: G 98 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7351 (mt-10) REVERT: G 133 THR cc_start: 0.6652 (m) cc_final: 0.6432 (p) REVERT: G 136 ARG cc_start: 0.7811 (mtt-85) cc_final: 0.7528 (mtt-85) REVERT: G 185 SER cc_start: 0.7135 (t) cc_final: 0.6883 (p) REVERT: G 192 LYS cc_start: 0.6344 (mmtm) cc_final: 0.6017 (mmmt) REVERT: G 194 ASP cc_start: 0.6933 (t70) cc_final: 0.6593 (m-30) REVERT: G 198 ARG cc_start: 0.6049 (ttp80) cc_final: 0.5825 (ttp80) REVERT: H 27 PHE cc_start: 0.7435 (m-80) cc_final: 0.6940 (m-80) REVERT: H 32 MET cc_start: 0.8078 (mpp) cc_final: 0.7817 (mpp) REVERT: H 78 SER cc_start: 0.7668 (p) cc_final: 0.7297 (t) REVERT: H 177 GLN cc_start: 0.3387 (tp40) cc_final: 0.2640 (mm-40) REVERT: H 197 GLN cc_start: 0.7998 (pm20) cc_final: 0.7741 (mp10) REVERT: H 217 MET cc_start: 0.6669 (tpp) cc_final: 0.5566 (ttt) REVERT: H 223 LYS cc_start: 0.6222 (mmpt) cc_final: 0.5828 (tptp) REVERT: h 4 GLN cc_start: 0.2500 (mm-40) cc_final: 0.2002 (tt0) REVERT: h 30 MET cc_start: 0.0478 (tpp) cc_final: -0.0234 (tpt) REVERT: h 42 MET cc_start: 0.5178 (tpt) cc_final: 0.4397 (ttt) REVERT: h 60 ARG cc_start: 0.6004 (mmm160) cc_final: 0.5713 (ttp80) REVERT: h 139 LYS cc_start: 0.5771 (mmmm) cc_final: 0.5559 (ttmt) REVERT: h 217 MET cc_start: 0.4204 (ppp) cc_final: 0.3823 (ptm) REVERT: h 247 TRP cc_start: 0.3668 (m-90) cc_final: 0.3103 (m-90) REVERT: I 18 GLU cc_start: 0.5617 (pp20) cc_final: 0.5146 (tm-30) REVERT: I 37 LYS cc_start: 0.4564 (mmtm) cc_final: 0.3737 (pttt) REVERT: I 43 LEU cc_start: 0.5095 (mm) cc_final: 0.4821 (mm) REVERT: I 58 LYS cc_start: 0.7470 (mtmt) cc_final: 0.7183 (mttm) REVERT: I 73 GLN cc_start: 0.7066 (mm-40) cc_final: 0.6807 (mm-40) REVERT: I 131 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7759 (tm-30) REVERT: I 148 LEU cc_start: 0.5728 (mm) cc_final: 0.5232 (mm) REVERT: I 155 LYS cc_start: 0.6308 (mttp) cc_final: 0.6086 (mmtm) REVERT: I 167 GLU cc_start: 0.7105 (tp30) cc_final: 0.6844 (tt0) REVERT: I 177 TYR cc_start: 0.6993 (t80) cc_final: 0.6691 (t80) REVERT: I 186 ASN cc_start: 0.7617 (t0) cc_final: 0.7367 (t0) REVERT: J 107 THR cc_start: 0.6799 (m) cc_final: 0.6519 (p) REVERT: J 111 GLN cc_start: 0.8240 (mt0) cc_final: 0.7774 (tp40) REVERT: J 121 LEU cc_start: 0.7416 (tp) cc_final: 0.6939 (tp) REVERT: J 154 LYS cc_start: 0.7439 (ptmm) cc_final: 0.6862 (mmtt) REVERT: J 165 GLN cc_start: 0.6617 (pt0) cc_final: 0.5858 (mm110) REVERT: J 203 LYS cc_start: 0.7565 (mtmm) cc_final: 0.6911 (tmtt) REVERT: n 20 MET cc_start: 0.7805 (tmm) cc_final: 0.6485 (ttm) REVERT: K 17 ARG cc_start: 0.6458 (tpt-90) cc_final: 0.6216 (tpt170) REVERT: K 55 LYS cc_start: 0.6370 (ttmt) cc_final: 0.5835 (mttm) REVERT: K 66 LYS cc_start: 0.7412 (mmpt) cc_final: 0.7092 (pttt) REVERT: K 79 ARG cc_start: 0.7239 (tpp80) cc_final: 0.6879 (mtt180) REVERT: K 96 TYR cc_start: 0.6654 (m-10) cc_final: 0.6352 (m-10) REVERT: K 138 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7613 (mtm110) REVERT: x 645 ILE cc_start: 0.5270 (pt) cc_final: 0.5068 (pt) REVERT: x 779 LYS cc_start: 0.6199 (mmpt) cc_final: 0.5833 (tptp) REVERT: x 847 ARG cc_start: 0.5957 (ttm110) cc_final: 0.5583 (ptm-80) REVERT: x 852 GLU cc_start: 0.5178 (pm20) cc_final: 0.4756 (mp0) REVERT: x 859 MET cc_start: 0.5385 (tmm) cc_final: 0.4435 (ttt) REVERT: x 882 GLU cc_start: 0.4918 (tp30) cc_final: 0.4477 (pp20) REVERT: x 884 ASP cc_start: 0.6014 (p0) cc_final: 0.5737 (p0) REVERT: x 908 MET cc_start: 0.4159 (pmm) cc_final: 0.3837 (ppp) REVERT: x 909 LYS cc_start: 0.5606 (ptpt) cc_final: 0.5356 (mmmm) REVERT: x 1001 VAL cc_start: 0.4356 (t) cc_final: 0.3741 (t) REVERT: x 1003 TYR cc_start: 0.4844 (p90) cc_final: 0.4514 (p90) REVERT: x 1026 ASP cc_start: 0.6929 (m-30) cc_final: 0.6713 (m-30) REVERT: x 1060 ILE cc_start: 0.5285 (pt) cc_final: 0.4910 (pt) REVERT: x 1072 GLN cc_start: 0.6889 (pp30) cc_final: 0.6603 (pp30) REVERT: x 1073 ASP cc_start: 0.7215 (m-30) cc_final: 0.6795 (t0) REVERT: x 1083 LYS cc_start: 0.6582 (tttt) cc_final: 0.6214 (pttm) REVERT: x 1108 MET cc_start: 0.2636 (tpt) cc_final: 0.2415 (ttm) REVERT: x 1162 ILE cc_start: 0.5657 (mt) cc_final: 0.5453 (mp) REVERT: x 1169 MET cc_start: 0.3390 (pmm) cc_final: 0.2570 (ttp) REVERT: x 1178 ASP cc_start: 0.1362 (t70) cc_final: 0.1101 (p0) REVERT: x 1206 GLN cc_start: 0.8484 (tp40) cc_final: 0.8156 (pt0) REVERT: L 20 VAL cc_start: 0.4437 (p) cc_final: 0.4235 (m) REVERT: L 49 MET cc_start: 0.5412 (ttm) cc_final: 0.5206 (ttm) REVERT: M 8 ARG cc_start: 0.5769 (mtp85) cc_final: 0.5569 (mtp85) REVERT: M 63 THR cc_start: 0.7099 (p) cc_final: 0.6701 (p) REVERT: M 65 ASN cc_start: 0.6776 (t0) cc_final: 0.6286 (p0) REVERT: M 67 SER cc_start: 0.8846 (t) cc_final: 0.8640 (p) REVERT: M 81 LYS cc_start: 0.6661 (ptmt) cc_final: 0.6205 (ttpt) REVERT: M 121 GLN cc_start: 0.6982 (mm-40) cc_final: 0.6631 (mm110) REVERT: M 135 SER cc_start: 0.7878 (t) cc_final: 0.7539 (t) REVERT: N 99 LYS cc_start: 0.2869 (pptt) cc_final: 0.2481 (pttm) REVERT: O 36 GLN cc_start: 0.7700 (mp10) cc_final: 0.6978 (tp40) REVERT: O 100 LYS cc_start: 0.7416 (tppt) cc_final: 0.6739 (tptp) REVERT: P 37 PHE cc_start: 0.8136 (m-80) cc_final: 0.7738 (m-80) REVERT: P 47 LEU cc_start: 0.8551 (tp) cc_final: 0.8271 (tp) REVERT: P 60 MET cc_start: 0.5781 (mmm) cc_final: 0.5574 (mmm) REVERT: P 130 GLU cc_start: 0.7603 (pm20) cc_final: 0.6660 (mt-10) REVERT: Q 20 VAL cc_start: 0.5599 (m) cc_final: 0.5394 (p) REVERT: R 32 ILE cc_start: 0.7328 (mm) cc_final: 0.6896 (mm) REVERT: R 42 ILE cc_start: 0.6939 (mm) cc_final: 0.6705 (mt) REVERT: R 61 GLU cc_start: 0.6787 (pm20) cc_final: 0.6525 (mp0) REVERT: R 106 LYS cc_start: 0.7260 (ttmm) cc_final: 0.6672 (ttmt) REVERT: R 116 ASP cc_start: 0.7691 (t70) cc_final: 0.7489 (m-30) REVERT: S 7 LYS cc_start: 0.6539 (pttt) cc_final: 0.6090 (pptt) REVERT: S 20 TYR cc_start: 0.4657 (m-80) cc_final: 0.4272 (m-10) REVERT: S 37 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7240 (tm-30) REVERT: S 98 VAL cc_start: 0.7610 (t) cc_final: 0.7164 (p) REVERT: T 7 GLU cc_start: 0.7300 (tp30) cc_final: 0.6974 (mt-10) REVERT: T 19 ASN cc_start: 0.5175 (m-40) cc_final: 0.4715 (p0) REVERT: T 40 TYR cc_start: 0.7155 (t80) cc_final: 0.6864 (t80) REVERT: T 43 VAL cc_start: 0.7793 (m) cc_final: 0.7447 (p) REVERT: T 75 ARG cc_start: 0.7499 (mtp180) cc_final: 0.6971 (mmm-85) REVERT: T 83 PHE cc_start: 0.6491 (t80) cc_final: 0.5975 (t80) REVERT: T 115 LYS cc_start: 0.4782 (tttm) cc_final: 0.4094 (mmmt) REVERT: T 127 TRP cc_start: 0.7220 (m-10) cc_final: 0.6933 (m100) REVERT: T 129 LEU cc_start: 0.6671 (mt) cc_final: 0.6350 (mp) REVERT: T 134 GLN cc_start: 0.6419 (mm110) cc_final: 0.5769 (mt0) REVERT: U 5 THR cc_start: 0.6879 (t) cc_final: 0.6524 (p) REVERT: U 28 LEU cc_start: 0.7962 (mp) cc_final: 0.7639 (pt) REVERT: U 36 THR cc_start: 0.6797 (t) cc_final: 0.6435 (p) REVERT: U 42 HIS cc_start: 0.6229 (p-80) cc_final: 0.5870 (p-80) REVERT: U 50 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6979 (mp0) REVERT: U 97 LYS cc_start: 0.5886 (pttm) cc_final: 0.5304 (ttmt) REVERT: U 105 GLN cc_start: 0.6914 (mt0) cc_final: 0.6657 (mm-40) REVERT: W 8 PHE cc_start: 0.6147 (m-80) cc_final: 0.5613 (t80) REVERT: W 36 VAL cc_start: 0.5693 (m) cc_final: 0.5455 (t) REVERT: W 76 ASP cc_start: 0.6341 (t70) cc_final: 0.5416 (t70) REVERT: W 78 ILE cc_start: 0.6652 (mm) cc_final: 0.6438 (mp) REVERT: X 12 LYS cc_start: 0.6834 (tppp) cc_final: 0.6542 (ttpt) REVERT: X 18 GLU cc_start: 0.7414 (tp30) cc_final: 0.7061 (pp20) REVERT: X 19 LYS cc_start: 0.7424 (mtpt) cc_final: 0.7089 (mtmt) REVERT: X 37 PHE cc_start: 0.7938 (t80) cc_final: 0.7653 (t80) REVERT: X 46 TYR cc_start: 0.7623 (m-10) cc_final: 0.6800 (m-80) REVERT: X 85 ASP cc_start: 0.7411 (m-30) cc_final: 0.7099 (m-30) REVERT: X 88 LYS cc_start: 0.7625 (ttmm) cc_final: 0.7224 (tmtt) REVERT: X 130 PHE cc_start: 0.7399 (p90) cc_final: 0.6615 (p90) REVERT: Y 25 LYS cc_start: 0.6157 (tppt) cc_final: 0.5755 (mmtm) REVERT: Y 134 TYR cc_start: 0.7126 (t80) cc_final: 0.6629 (t80) outliers start: 3 outliers final: 0 residues processed: 1478 average time/residue: 0.9318 time to fit residues: 2249.7335 Evaluate side-chains 852 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 852 time to evaluate : 5.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 630 optimal weight: 8.9990 chunk 566 optimal weight: 20.0000 chunk 314 optimal weight: 0.3980 chunk 193 optimal weight: 0.9980 chunk 381 optimal weight: 0.1980 chunk 302 optimal weight: 20.0000 chunk 585 optimal weight: 30.0000 chunk 226 optimal weight: 10.0000 chunk 356 optimal weight: 3.9990 chunk 435 optimal weight: 6.9990 chunk 678 optimal weight: 20.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS a 45 ASN a 112 ASN B 50 ASN B 169 HIS B 193 HIS C 157 GLN c 51 GLN D 136 HIS ** e 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN F 216 ASN F 224 ASN ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN H 70 HIS H 202 ASN h 159 ASN J 155 ASN x 712 ASN x 824 HIS x1079 GLN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN P 26 ASN R 8 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN T 101 ASN ** T 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 93743 Z= 0.182 Angle : 0.576 9.763 136219 Z= 0.289 Chirality : 0.035 0.283 16874 Planarity : 0.005 0.082 9815 Dihedral : 22.857 178.978 37727 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.45 % Allowed : 11.50 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.46 (0.11), residues: 5551 helix: -0.23 (0.12), residues: 1720 sheet: -0.54 (0.17), residues: 942 loop : -1.58 (0.11), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP h 17 HIS 0.009 0.001 HIS Q 128 PHE 0.027 0.002 PHE h 65 TYR 0.019 0.001 TYR e 34 ARG 0.016 0.001 ARG h 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 890 time to evaluate : 6.873 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: Z 74 MET cc_start: 0.7635 (ptp) cc_final: 0.7103 (ptp) REVERT: A 46 ARG cc_start: 0.4996 (mtm180) cc_final: 0.4442 (ptp-170) REVERT: A 61 ILE cc_start: 0.7143 (mm) cc_final: 0.6834 (tp) REVERT: a 52 LYS cc_start: 0.7612 (tptp) cc_final: 0.6973 (ptmm) REVERT: a 78 LYS cc_start: 0.6664 (mttp) cc_final: 0.6320 (mmtm) REVERT: a 112 ASN cc_start: 0.5676 (m110) cc_final: 0.5147 (p0) REVERT: B 14 ASP cc_start: 0.7596 (m-30) cc_final: 0.7223 (m-30) REVERT: B 80 ARG cc_start: 0.6753 (mmm-85) cc_final: 0.6021 (tpt170) REVERT: B 112 ILE cc_start: 0.8033 (pt) cc_final: 0.7770 (pt) REVERT: B 132 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6601 (mt0) REVERT: B 136 GLU cc_start: 0.7908 (tp30) cc_final: 0.7431 (tp30) REVERT: B 155 ARG cc_start: 0.7490 (ttm170) cc_final: 0.7250 (ttm170) REVERT: B 205 ARG cc_start: 0.5740 (OUTLIER) cc_final: 0.5209 (ptm160) REVERT: b 68 TYR cc_start: 0.7448 (m-80) cc_final: 0.7071 (m-80) REVERT: b 82 LYS cc_start: 0.8212 (mmtm) cc_final: 0.7884 (mmtp) REVERT: b 88 SER cc_start: 0.6810 (p) cc_final: 0.6326 (t) REVERT: C 30 TRP cc_start: 0.7376 (m100) cc_final: 0.6837 (m100) REVERT: C 34 LYS cc_start: 0.5801 (mmtt) cc_final: 0.5383 (mmtt) REVERT: C 107 ARG cc_start: 0.6877 (mmm-85) cc_final: 0.6221 (ttm170) REVERT: c 15 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6799 (mm-30) REVERT: D 101 SER cc_start: 0.6599 (m) cc_final: 0.5920 (t) REVERT: D 176 LYS cc_start: 0.7830 (mtpp) cc_final: 0.7407 (mmtt) REVERT: D 215 MET cc_start: 0.7128 (ptp) cc_final: 0.6876 (ttp) REVERT: D 230 THR cc_start: 0.6476 (m) cc_final: 0.6166 (p) REVERT: d 10 LYS cc_start: 0.6661 (tttm) cc_final: 0.6095 (mttm) REVERT: d 16 LYS cc_start: 0.6646 (ptmt) cc_final: 0.6416 (ptpt) REVERT: E 17 PHE cc_start: 0.6262 (t80) cc_final: 0.5996 (t80) REVERT: E 40 ARG cc_start: 0.5744 (ttt180) cc_final: 0.4899 (mmt180) REVERT: E 72 VAL cc_start: 0.7024 (t) cc_final: 0.6770 (t) REVERT: E 117 ARG cc_start: 0.6046 (mmm160) cc_final: 0.5007 (mmt180) REVERT: E 157 MET cc_start: 0.7104 (tpp) cc_final: 0.6488 (ptp) REVERT: E 169 ASP cc_start: 0.6723 (m-30) cc_final: 0.6435 (m-30) REVERT: E 187 LYS cc_start: 0.5591 (mtmm) cc_final: 0.5095 (tttm) REVERT: F 54 TYR cc_start: 0.8102 (m-10) cc_final: 0.7249 (m-10) REVERT: F 62 LYS cc_start: 0.6647 (tptt) cc_final: 0.6381 (tppt) REVERT: F 64 ILE cc_start: 0.7647 (mm) cc_final: 0.7360 (mt) REVERT: F 87 MET cc_start: 0.8418 (tpp) cc_final: 0.8095 (tpp) REVERT: f 129 ASN cc_start: 0.6480 (t0) cc_final: 0.6221 (t0) REVERT: G 25 THR cc_start: 0.7503 (t) cc_final: 0.7281 (t) REVERT: G 28 VAL cc_start: 0.5873 (m) cc_final: 0.5444 (m) REVERT: G 42 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7133 (tptt) REVERT: G 98 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7523 (mt-10) REVERT: G 185 SER cc_start: 0.7232 (t) cc_final: 0.6936 (p) REVERT: G 192 LYS cc_start: 0.6172 (mmtm) cc_final: 0.5781 (mmmt) REVERT: G 194 ASP cc_start: 0.6996 (t70) cc_final: 0.6507 (m-30) REVERT: G 198 ARG cc_start: 0.6133 (ttp80) cc_final: 0.5904 (ttp80) REVERT: H 14 LYS cc_start: 0.6244 (OUTLIER) cc_final: 0.5779 (tptp) REVERT: H 32 MET cc_start: 0.7905 (mpp) cc_final: 0.7545 (mpp) REVERT: H 124 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5853 (mp) REVERT: H 217 MET cc_start: 0.6440 (tpp) cc_final: 0.5277 (ttt) REVERT: H 223 LYS cc_start: 0.5941 (mmpt) cc_final: 0.5606 (tmtt) REVERT: h 4 GLN cc_start: 0.2526 (mm-40) cc_final: 0.1874 (tt0) REVERT: h 5 MET cc_start: 0.3529 (mmt) cc_final: 0.3262 (mmt) REVERT: h 30 MET cc_start: 0.0543 (tpp) cc_final: 0.0281 (tpt) REVERT: h 42 MET cc_start: 0.5198 (tpt) cc_final: 0.4775 (ttt) REVERT: h 60 ARG cc_start: 0.6256 (mmm160) cc_final: 0.5972 (ttp80) REVERT: h 139 LYS cc_start: 0.5846 (mmmm) cc_final: 0.5552 (ttmt) REVERT: h 177 TRP cc_start: 0.5934 (m-90) cc_final: 0.5505 (m-90) REVERT: h 217 MET cc_start: 0.3916 (ppp) cc_final: 0.3589 (ptm) REVERT: I 18 GLU cc_start: 0.5362 (pp20) cc_final: 0.5156 (tm-30) REVERT: I 37 LYS cc_start: 0.4810 (mmtm) cc_final: 0.4048 (pttt) REVERT: I 131 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7715 (tm-30) REVERT: I 148 LEU cc_start: 0.6008 (mm) cc_final: 0.5394 (mm) REVERT: J 109 TYR cc_start: 0.7257 (m-80) cc_final: 0.6993 (m-80) REVERT: J 111 GLN cc_start: 0.8260 (mt0) cc_final: 0.7916 (tp40) REVERT: J 154 LYS cc_start: 0.7364 (ptmm) cc_final: 0.7023 (mmtt) REVERT: J 165 GLN cc_start: 0.6105 (pt0) cc_final: 0.5629 (mm-40) REVERT: J 203 LYS cc_start: 0.7605 (mtmm) cc_final: 0.7048 (tmtt) REVERT: K 17 ARG cc_start: 0.6384 (tpt-90) cc_final: 0.6155 (tpt170) REVERT: K 55 LYS cc_start: 0.6514 (ttmt) cc_final: 0.5870 (mttm) REVERT: K 75 ASN cc_start: 0.6751 (t0) cc_final: 0.6172 (t0) REVERT: K 79 ARG cc_start: 0.7102 (tpp80) cc_final: 0.6416 (mpt180) REVERT: K 89 GLU cc_start: 0.7908 (tp30) cc_final: 0.6886 (tp30) REVERT: K 135 ILE cc_start: 0.8446 (mp) cc_final: 0.8190 (mm) REVERT: x 779 LYS cc_start: 0.6177 (mmpt) cc_final: 0.5774 (tptt) REVERT: x 859 MET cc_start: 0.5642 (tmm) cc_final: 0.5198 (ttt) REVERT: x 909 LYS cc_start: 0.5612 (ptpt) cc_final: 0.5361 (pttp) REVERT: x 1017 MET cc_start: 0.6997 (tpt) cc_final: 0.6680 (ttt) REVERT: x 1058 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7277 (mt-10) REVERT: x 1073 ASP cc_start: 0.7178 (m-30) cc_final: 0.6276 (t0) REVERT: x 1083 LYS cc_start: 0.6522 (tttt) cc_final: 0.6179 (pttm) REVERT: x 1178 ASP cc_start: 0.1823 (t70) cc_final: 0.1377 (p0) REVERT: x 1200 MET cc_start: 0.1242 (ppp) cc_final: 0.0831 (ppp) REVERT: x 1206 GLN cc_start: 0.8490 (tp40) cc_final: 0.8165 (pt0) REVERT: M 67 SER cc_start: 0.8966 (t) cc_final: 0.8655 (m) REVERT: N 99 LYS cc_start: 0.2961 (pptt) cc_final: 0.2570 (pttm) REVERT: O 100 LYS cc_start: 0.7643 (tppt) cc_final: 0.7023 (tptp) REVERT: P 37 PHE cc_start: 0.8166 (m-80) cc_final: 0.7749 (m-80) REVERT: P 60 MET cc_start: 0.6145 (mmm) cc_final: 0.5908 (mmm) REVERT: P 135 ILE cc_start: 0.7859 (tt) cc_final: 0.7589 (tt) REVERT: R 42 ILE cc_start: 0.7236 (mm) cc_final: 0.6866 (mt) REVERT: R 45 ARG cc_start: 0.6974 (mmm160) cc_final: 0.5585 (mmp-170) REVERT: R 53 GLU cc_start: 0.7510 (tp30) cc_final: 0.7144 (mt-10) REVERT: R 116 ASP cc_start: 0.7653 (t70) cc_final: 0.7402 (m-30) REVERT: S 7 LYS cc_start: 0.6505 (pttt) cc_final: 0.6121 (pptt) REVERT: S 18 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6109 (mm-30) REVERT: S 20 TYR cc_start: 0.4777 (m-80) cc_final: 0.4296 (m-80) REVERT: S 98 VAL cc_start: 0.7410 (t) cc_final: 0.7101 (p) REVERT: T 19 ASN cc_start: 0.5229 (m-40) cc_final: 0.4831 (p0) REVERT: T 115 LYS cc_start: 0.5165 (tttm) cc_final: 0.4444 (mmmt) REVERT: T 127 TRP cc_start: 0.7436 (m-10) cc_final: 0.7023 (m100) REVERT: T 134 GLN cc_start: 0.6247 (mm110) cc_final: 0.5577 (mt0) REVERT: U 5 THR cc_start: 0.6918 (t) cc_final: 0.6540 (p) REVERT: U 28 LEU cc_start: 0.7867 (mp) cc_final: 0.7632 (pt) REVERT: U 36 THR cc_start: 0.6681 (t) cc_final: 0.6324 (t) REVERT: U 50 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7042 (mp0) REVERT: U 97 LYS cc_start: 0.5938 (pttm) cc_final: 0.5520 (ttmt) REVERT: U 105 GLN cc_start: 0.7244 (mt0) cc_final: 0.6981 (mm-40) REVERT: V 40 ILE cc_start: 0.6282 (mm) cc_final: 0.6057 (mt) REVERT: W 8 PHE cc_start: 0.6311 (m-80) cc_final: 0.5620 (t80) REVERT: W 21 ASN cc_start: 0.7277 (t0) cc_final: 0.6225 (t0) REVERT: X 12 LYS cc_start: 0.6698 (tppp) cc_final: 0.6310 (ttpt) REVERT: X 18 GLU cc_start: 0.7353 (tp30) cc_final: 0.7004 (pp20) REVERT: X 19 LYS cc_start: 0.7361 (mtpt) cc_final: 0.7059 (mtmt) REVERT: X 32 LYS cc_start: 0.8861 (tppt) cc_final: 0.8192 (mtpt) REVERT: X 46 TYR cc_start: 0.8186 (m-10) cc_final: 0.7353 (m-80) REVERT: X 55 ASP cc_start: 0.6900 (p0) cc_final: 0.6513 (p0) REVERT: X 88 LYS cc_start: 0.7670 (ttmm) cc_final: 0.7080 (tmtt) REVERT: Y 92 ASN cc_start: 0.7109 (p0) cc_final: 0.6856 (p0) REVERT: Y 134 TYR cc_start: 0.7374 (t80) cc_final: 0.6872 (t80) outliers start: 119 outliers final: 78 residues processed: 960 average time/residue: 0.8596 time to fit residues: 1393.9926 Evaluate side-chains 818 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 736 time to evaluate : 5.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 40 ILE Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 156 TYR Chi-restraints excluded: chain h residue 40 ILE Chi-restraints excluded: chain h residue 91 ASP Chi-restraints excluded: chain h residue 196 ASN Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 153 LYS Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain x residue 652 THR Chi-restraints excluded: chain x residue 673 LEU Chi-restraints excluded: chain x residue 710 LEU Chi-restraints excluded: chain x residue 742 LEU Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 756 ILE Chi-restraints excluded: chain x residue 796 PHE Chi-restraints excluded: chain x residue 877 ASN Chi-restraints excluded: chain x residue 892 GLU Chi-restraints excluded: chain x residue 903 LEU Chi-restraints excluded: chain x residue 943 LEU Chi-restraints excluded: chain x residue 999 SER Chi-restraints excluded: chain x residue 1031 VAL Chi-restraints excluded: chain x residue 1099 ILE Chi-restraints excluded: chain x residue 1118 LYS Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 27 ASP Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 108 GLU Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain X residue 96 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 377 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 564 optimal weight: 40.0000 chunk 461 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 679 optimal weight: 0.7980 chunk 734 optimal weight: 6.9990 chunk 605 optimal weight: 20.0000 chunk 673 optimal weight: 20.0000 chunk 231 optimal weight: 8.9990 chunk 545 optimal weight: 7.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 106 GLN a 45 ASN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN h 14 HIS h 104 HIS h 215 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 HIS K 134 HIS ** x 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x1079 GLN x1173 HIS N 72 HIS N 75 ASN O 62 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN ** T 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 42 HIS X 92 ASN Y 77 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 93743 Z= 0.312 Angle : 0.702 13.419 136219 Z= 0.354 Chirality : 0.040 0.273 16874 Planarity : 0.006 0.096 9815 Dihedral : 22.864 176.502 37727 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.97 % Allowed : 16.73 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.50 (0.11), residues: 5551 helix: -0.02 (0.12), residues: 1713 sheet: -0.87 (0.16), residues: 932 loop : -1.65 (0.11), residues: 2906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP x 762 HIS 0.014 0.002 HIS h 64 PHE 0.045 0.003 PHE D 236 TYR 0.024 0.002 TYR e 34 ARG 0.010 0.001 ARG I 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 788 time to evaluate : 5.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 74 MET cc_start: 0.8124 (ptp) cc_final: 0.7774 (ptp) REVERT: A 46 ARG cc_start: 0.5169 (mtm180) cc_final: 0.4468 (ptp-170) REVERT: A 48 GLU cc_start: 0.6102 (tm-30) cc_final: 0.5848 (tm-30) REVERT: a 52 LYS cc_start: 0.7455 (tptp) cc_final: 0.6733 (ptmm) REVERT: a 78 LYS cc_start: 0.6622 (mttp) cc_final: 0.6194 (mmtm) REVERT: a 94 LYS cc_start: 0.5527 (tmmt) cc_final: 0.5194 (mmtp) REVERT: a 112 ASN cc_start: 0.5911 (m110) cc_final: 0.5097 (p0) REVERT: B 80 ARG cc_start: 0.6938 (mmm-85) cc_final: 0.6137 (mmt180) REVERT: B 128 ARG cc_start: 0.7466 (tpp-160) cc_final: 0.6702 (mmm160) REVERT: B 132 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6900 (tt0) REVERT: B 155 ARG cc_start: 0.7603 (ttm170) cc_final: 0.7191 (ttp-170) REVERT: B 174 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7819 (mmm) REVERT: b 33 ASP cc_start: 0.8586 (p0) cc_final: 0.8302 (p0) REVERT: b 79 ILE cc_start: 0.7310 (mm) cc_final: 0.7104 (mp) REVERT: b 94 ASP cc_start: 0.5973 (m-30) cc_final: 0.5723 (m-30) REVERT: C 38 MET cc_start: 0.7087 (ptp) cc_final: 0.6673 (ptp) REVERT: C 107 ARG cc_start: 0.7089 (mmm-85) cc_final: 0.6501 (ttm170) REVERT: c 64 CYS cc_start: 0.8209 (m) cc_final: 0.7881 (p) REVERT: D 108 LYS cc_start: 0.5782 (ttmt) cc_final: 0.5227 (ttpp) REVERT: D 120 GLN cc_start: 0.6840 (pt0) cc_final: 0.6481 (pt0) REVERT: D 215 MET cc_start: 0.7851 (ptp) cc_final: 0.7368 (ttp) REVERT: d 10 LYS cc_start: 0.6436 (tttm) cc_final: 0.5923 (mttt) REVERT: d 16 LYS cc_start: 0.6803 (ptmt) cc_final: 0.6461 (ptpt) REVERT: d 62 GLU cc_start: 0.7465 (pm20) cc_final: 0.7015 (pm20) REVERT: E 17 PHE cc_start: 0.6436 (t80) cc_final: 0.6098 (t80) REVERT: E 40 ARG cc_start: 0.5751 (ttt180) cc_final: 0.4913 (mmt180) REVERT: E 72 VAL cc_start: 0.7243 (t) cc_final: 0.7031 (t) REVERT: E 169 ASP cc_start: 0.6878 (m-30) cc_final: 0.6613 (m-30) REVERT: E 188 ILE cc_start: 0.7827 (mm) cc_final: 0.7290 (tp) REVERT: E 226 GLN cc_start: 0.5140 (OUTLIER) cc_final: 0.3193 (pt0) REVERT: e 12 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6350 (mmp80) REVERT: F 54 TYR cc_start: 0.8403 (m-10) cc_final: 0.8202 (m-10) REVERT: F 168 LYS cc_start: 0.7179 (mmmt) cc_final: 0.6749 (mttm) REVERT: F 250 GLU cc_start: 0.8132 (mp0) cc_final: 0.7924 (mp0) REVERT: G 42 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7712 (mttp) REVERT: G 114 ASN cc_start: 0.7419 (t0) cc_final: 0.7174 (t0) REVERT: G 198 ARG cc_start: 0.6267 (ttp80) cc_final: 0.5935 (ttp80) REVERT: H 106 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7822 (tt) REVERT: H 217 MET cc_start: 0.6541 (tpp) cc_final: 0.5338 (ttt) REVERT: H 223 LYS cc_start: 0.5799 (mmpt) cc_final: 0.5452 (tmtt) REVERT: h 4 GLN cc_start: 0.2587 (mm-40) cc_final: 0.1880 (tt0) REVERT: h 29 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.4338 (t0) REVERT: h 30 MET cc_start: 0.0771 (tpp) cc_final: 0.0420 (tpt) REVERT: h 139 LYS cc_start: 0.5640 (mmmm) cc_final: 0.5373 (ttmt) REVERT: h 217 MET cc_start: 0.4091 (ppp) cc_final: 0.3703 (ptm) REVERT: h 247 TRP cc_start: 0.4390 (m-90) cc_final: 0.4166 (m-90) REVERT: h 304 ASP cc_start: 0.7210 (t0) cc_final: 0.6582 (p0) REVERT: I 37 LYS cc_start: 0.4654 (mmtm) cc_final: 0.4068 (pttt) REVERT: J 165 GLN cc_start: 0.6657 (pt0) cc_final: 0.5718 (mm-40) REVERT: n 1 MET cc_start: 0.7531 (tpp) cc_final: 0.7059 (tpt) REVERT: n 21 ARG cc_start: 0.5054 (ttm170) cc_final: 0.4775 (ttp-110) REVERT: K 55 LYS cc_start: 0.6538 (ttmt) cc_final: 0.5901 (mttm) REVERT: K 66 LYS cc_start: 0.8172 (tttt) cc_final: 0.7639 (mttp) REVERT: K 75 ASN cc_start: 0.6563 (t0) cc_final: 0.6177 (t0) REVERT: K 79 ARG cc_start: 0.7254 (tpp80) cc_final: 0.6692 (mmp80) REVERT: K 92 MET cc_start: 0.7089 (mmt) cc_final: 0.6702 (mmt) REVERT: x 763 LYS cc_start: 0.6620 (ptpp) cc_final: 0.6314 (mmtm) REVERT: x 779 LYS cc_start: 0.6188 (mmpt) cc_final: 0.5754 (tptt) REVERT: x 909 LYS cc_start: 0.5394 (ptpt) cc_final: 0.5183 (pttp) REVERT: x 1006 ILE cc_start: 0.6379 (pt) cc_final: 0.5765 (mm) REVERT: x 1073 ASP cc_start: 0.6961 (m-30) cc_final: 0.6569 (t0) REVERT: x 1083 LYS cc_start: 0.6272 (tttt) cc_final: 0.5940 (pttm) REVERT: x 1178 ASP cc_start: 0.2977 (t70) cc_final: 0.1914 (p0) REVERT: x 1206 GLN cc_start: 0.8433 (tp40) cc_final: 0.8167 (pt0) REVERT: L 27 VAL cc_start: 0.7267 (m) cc_final: 0.6924 (p) REVERT: M 5 GLN cc_start: 0.7419 (mp10) cc_final: 0.7051 (mp10) REVERT: M 7 GLU cc_start: 0.7991 (pm20) cc_final: 0.7527 (pm20) REVERT: M 67 SER cc_start: 0.8824 (t) cc_final: 0.8416 (m) REVERT: N 66 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5661 (mt-10) REVERT: N 78 LYS cc_start: 0.4616 (mmtt) cc_final: 0.4114 (pttp) REVERT: N 99 LYS cc_start: 0.2934 (pptt) cc_final: 0.2627 (pttm) REVERT: O 32 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.6689 (t0) REVERT: O 100 LYS cc_start: 0.7894 (tppt) cc_final: 0.7401 (tptp) REVERT: P 37 PHE cc_start: 0.8214 (m-80) cc_final: 0.7842 (m-80) REVERT: P 103 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7108 (p0) REVERT: P 138 ASP cc_start: 0.5517 (OUTLIER) cc_final: 0.5247 (p0) REVERT: R 42 ILE cc_start: 0.7857 (mm) cc_final: 0.7603 (mt) REVERT: R 116 ASP cc_start: 0.7788 (t70) cc_final: 0.7565 (m-30) REVERT: S 7 LYS cc_start: 0.6588 (pttt) cc_final: 0.6270 (pptt) REVERT: S 98 VAL cc_start: 0.7207 (t) cc_final: 0.6888 (p) REVERT: T 19 ASN cc_start: 0.5592 (m-40) cc_final: 0.5169 (p0) REVERT: T 71 MET cc_start: 0.7081 (tmm) cc_final: 0.6788 (tmm) REVERT: T 127 TRP cc_start: 0.7227 (m-10) cc_final: 0.7011 (m100) REVERT: T 134 GLN cc_start: 0.6133 (mm110) cc_final: 0.5431 (mm-40) REVERT: U 5 THR cc_start: 0.6990 (t) cc_final: 0.6666 (p) REVERT: U 28 LEU cc_start: 0.7805 (mp) cc_final: 0.7563 (pt) REVERT: U 105 GLN cc_start: 0.7305 (mt0) cc_final: 0.6975 (mm-40) REVERT: U 126 GLN cc_start: 0.7345 (mm-40) cc_final: 0.6770 (tm-30) REVERT: V 22 ILE cc_start: 0.5699 (mp) cc_final: 0.5453 (mp) REVERT: V 82 MET cc_start: 0.8507 (mtt) cc_final: 0.7960 (tpp) REVERT: X 12 LYS cc_start: 0.6628 (tppp) cc_final: 0.6316 (ttpt) REVERT: X 32 LYS cc_start: 0.8972 (tppt) cc_final: 0.8131 (ttpt) REVERT: X 88 LYS cc_start: 0.7640 (ttmm) cc_final: 0.7136 (tmtt) REVERT: X 112 ASP cc_start: 0.7862 (p0) cc_final: 0.7088 (p0) REVERT: Y 92 ASN cc_start: 0.6711 (p0) cc_final: 0.6465 (p0) REVERT: Y 93 PHE cc_start: 0.7432 (m-10) cc_final: 0.7212 (m-10) outliers start: 193 outliers final: 123 residues processed: 915 average time/residue: 0.8213 time to fit residues: 1287.8492 Evaluate side-chains 808 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 675 time to evaluate : 6.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 226 GLN Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 197 GLN Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 29 ASP Chi-restraints excluded: chain h residue 40 ILE Chi-restraints excluded: chain h residue 91 ASP Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 196 ASN Chi-restraints excluded: chain h residue 273 GLU Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 153 LYS Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain x residue 652 THR Chi-restraints excluded: chain x residue 673 LEU Chi-restraints excluded: chain x residue 742 LEU Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 877 ASN Chi-restraints excluded: chain x residue 943 LEU Chi-restraints excluded: chain x residue 999 SER Chi-restraints excluded: chain x residue 1001 VAL Chi-restraints excluded: chain x residue 1028 GLN Chi-restraints excluded: chain x residue 1042 ASP Chi-restraints excluded: chain x residue 1053 ARG Chi-restraints excluded: chain x residue 1060 ILE Chi-restraints excluded: chain x residue 1072 GLN Chi-restraints excluded: chain x residue 1118 LYS Chi-restraints excluded: chain x residue 1166 SER Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 125 HIS Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 108 GLU Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain Y residue 77 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 671 optimal weight: 6.9990 chunk 510 optimal weight: 20.0000 chunk 352 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 456 optimal weight: 9.9990 chunk 682 optimal weight: 2.9990 chunk 722 optimal weight: 2.9990 chunk 356 optimal weight: 1.9990 chunk 646 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 45 ASN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN F 50 ASN F 216 ASN h 14 HIS ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN x 777 GLN x 877 ASN x1062 HIS O 36 GLN O 58 HIS ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN R 97 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN T 101 ASN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 93743 Z= 0.199 Angle : 0.568 12.185 136219 Z= 0.288 Chirality : 0.036 0.279 16874 Planarity : 0.004 0.055 9815 Dihedral : 22.712 178.304 37727 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.60 % Allowed : 19.14 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.24 (0.11), residues: 5551 helix: 0.36 (0.13), residues: 1713 sheet: -0.78 (0.17), residues: 926 loop : -1.58 (0.11), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP h 17 HIS 0.008 0.001 HIS x1025 PHE 0.025 0.001 PHE x1196 TYR 0.022 0.001 TYR B 156 ARG 0.007 0.000 ARG x1053 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 751 time to evaluate : 5.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 74 MET cc_start: 0.8008 (ptp) cc_final: 0.7726 (ptp) REVERT: A 46 ARG cc_start: 0.5155 (mtm180) cc_final: 0.4487 (ptp-170) REVERT: A 48 GLU cc_start: 0.5781 (tm-30) cc_final: 0.5438 (tm-30) REVERT: a 52 LYS cc_start: 0.7476 (tptp) cc_final: 0.6764 (pttp) REVERT: a 78 LYS cc_start: 0.6596 (mttp) cc_final: 0.6162 (mmtm) REVERT: a 94 LYS cc_start: 0.5610 (tmmt) cc_final: 0.5268 (mmtp) REVERT: a 112 ASN cc_start: 0.5778 (m110) cc_final: 0.4917 (p0) REVERT: B 80 ARG cc_start: 0.6911 (mmm-85) cc_final: 0.6187 (tpt170) REVERT: B 132 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6808 (tt0) REVERT: b 33 ASP cc_start: 0.8541 (p0) cc_final: 0.8180 (p0) REVERT: b 94 ASP cc_start: 0.5976 (m-30) cc_final: 0.5739 (m-30) REVERT: C 43 ASN cc_start: 0.6109 (m-40) cc_final: 0.5399 (p0) REVERT: C 107 ARG cc_start: 0.7022 (mmm-85) cc_final: 0.6539 (ttm170) REVERT: C 224 GLU cc_start: 0.6215 (pp20) cc_final: 0.5604 (mm-30) REVERT: c 15 GLU cc_start: 0.7213 (tp30) cc_final: 0.6405 (mm-30) REVERT: D 105 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: D 108 LYS cc_start: 0.5659 (ttmt) cc_final: 0.5212 (ttpp) REVERT: D 215 MET cc_start: 0.7853 (ptp) cc_final: 0.7485 (ttp) REVERT: D 250 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.7182 (t80) REVERT: d 10 LYS cc_start: 0.6480 (tttm) cc_final: 0.5987 (mttt) REVERT: E 17 PHE cc_start: 0.6298 (t80) cc_final: 0.5955 (t80) REVERT: E 40 ARG cc_start: 0.5909 (ttt180) cc_final: 0.5087 (mmt180) REVERT: E 72 VAL cc_start: 0.7281 (t) cc_final: 0.7076 (t) REVERT: E 188 ILE cc_start: 0.7893 (mm) cc_final: 0.7621 (mm) REVERT: e 12 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6283 (mmp80) REVERT: F 66 MET cc_start: 0.7026 (ppp) cc_final: 0.5919 (tpt) REVERT: F 168 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6737 (mttm) REVERT: F 250 GLU cc_start: 0.8141 (mp0) cc_final: 0.7902 (mp0) REVERT: f 86 ARG cc_start: 0.7617 (ttt90) cc_final: 0.7133 (ttm-80) REVERT: G 42 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7766 (mttp) REVERT: G 114 ASN cc_start: 0.7369 (t0) cc_final: 0.7166 (t0) REVERT: G 185 SER cc_start: 0.7682 (t) cc_final: 0.7392 (p) REVERT: G 198 ARG cc_start: 0.6343 (ttp80) cc_final: 0.6005 (ttp80) REVERT: H 32 MET cc_start: 0.8230 (mpp) cc_final: 0.7722 (mpp) REVERT: H 106 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7911 (tt) REVERT: H 124 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6282 (mp) REVERT: H 217 MET cc_start: 0.6467 (tpp) cc_final: 0.5313 (ttt) REVERT: H 223 LYS cc_start: 0.5732 (mmpt) cc_final: 0.5386 (tptp) REVERT: h 139 LYS cc_start: 0.5627 (mmmm) cc_final: 0.5374 (ttmt) REVERT: h 217 MET cc_start: 0.4073 (ppp) cc_final: 0.3708 (ptm) REVERT: h 304 ASP cc_start: 0.7269 (t0) cc_final: 0.6631 (p0) REVERT: I 32 MET cc_start: 0.5223 (tpt) cc_final: 0.4854 (mtp) REVERT: I 37 LYS cc_start: 0.4678 (mmtm) cc_final: 0.4081 (pttt) REVERT: I 173 PHE cc_start: 0.7048 (m-80) cc_final: 0.6844 (m-80) REVERT: J 165 GLN cc_start: 0.6701 (pt0) cc_final: 0.5762 (mm-40) REVERT: n 21 ARG cc_start: 0.5035 (ttm170) cc_final: 0.4786 (ttp-110) REVERT: K 27 GLN cc_start: 0.7646 (tt0) cc_final: 0.7424 (tp40) REVERT: K 55 LYS cc_start: 0.6523 (ttmt) cc_final: 0.5976 (mttm) REVERT: K 66 LYS cc_start: 0.8292 (tttt) cc_final: 0.7898 (mttm) REVERT: K 75 ASN cc_start: 0.6447 (t0) cc_final: 0.5889 (t0) REVERT: K 79 ARG cc_start: 0.7366 (tpp80) cc_final: 0.6833 (mmp80) REVERT: K 117 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7806 (mm) REVERT: K 155 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7722 (mmtp) REVERT: x 763 LYS cc_start: 0.6475 (ptpp) cc_final: 0.6053 (mmtm) REVERT: x 843 MET cc_start: 0.4318 (ppp) cc_final: 0.3821 (ptm) REVERT: x 847 ARG cc_start: 0.5263 (ttm110) cc_final: 0.4385 (tmt170) REVERT: x 909 LYS cc_start: 0.5240 (ptpt) cc_final: 0.5028 (pttp) REVERT: x 1006 ILE cc_start: 0.6447 (pt) cc_final: 0.5798 (mm) REVERT: x 1073 ASP cc_start: 0.6876 (m-30) cc_final: 0.6478 (t0) REVERT: x 1083 LYS cc_start: 0.6403 (tttt) cc_final: 0.6080 (pttm) REVERT: x 1178 ASP cc_start: 0.3222 (t70) cc_final: 0.2178 (p0) REVERT: x 1206 GLN cc_start: 0.8480 (tp40) cc_final: 0.8219 (pt0) REVERT: L 27 VAL cc_start: 0.7441 (m) cc_final: 0.7123 (p) REVERT: M 7 GLU cc_start: 0.7970 (pm20) cc_final: 0.7533 (pm20) REVERT: M 67 SER cc_start: 0.8865 (t) cc_final: 0.8411 (m) REVERT: N 99 LYS cc_start: 0.3098 (pptt) cc_final: 0.2745 (pttm) REVERT: O 38 TYR cc_start: 0.6320 (m-80) cc_final: 0.5997 (m-80) REVERT: O 100 LYS cc_start: 0.7901 (tppt) cc_final: 0.7556 (tttm) REVERT: P 37 PHE cc_start: 0.8238 (m-80) cc_final: 0.7946 (m-10) REVERT: P 87 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.5649 (pt0) REVERT: P 138 ASP cc_start: 0.5342 (OUTLIER) cc_final: 0.5066 (p0) REVERT: Q 28 MET cc_start: 0.5531 (OUTLIER) cc_final: 0.5057 (tmm) REVERT: Q 30 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.4855 (t80) REVERT: Q 59 ARG cc_start: 0.4778 (tmt-80) cc_final: 0.4314 (ttm170) REVERT: R 41 MET cc_start: 0.7387 (tpp) cc_final: 0.7093 (tpp) REVERT: R 42 ILE cc_start: 0.7891 (mm) cc_final: 0.7605 (mt) REVERT: R 116 ASP cc_start: 0.7789 (t70) cc_final: 0.7589 (m-30) REVERT: S 7 LYS cc_start: 0.6591 (pttt) cc_final: 0.6270 (pptt) REVERT: S 18 GLU cc_start: 0.6549 (mt-10) cc_final: 0.6114 (mm-30) REVERT: S 98 VAL cc_start: 0.7166 (t) cc_final: 0.6828 (p) REVERT: T 19 ASN cc_start: 0.5847 (m-40) cc_final: 0.5359 (p0) REVERT: T 83 PHE cc_start: 0.6610 (t80) cc_final: 0.6120 (t80) REVERT: T 127 TRP cc_start: 0.7250 (m-10) cc_final: 0.7033 (m100) REVERT: T 134 GLN cc_start: 0.6176 (mm110) cc_final: 0.5440 (mt0) REVERT: U 5 THR cc_start: 0.7077 (t) cc_final: 0.6773 (p) REVERT: U 28 LEU cc_start: 0.7786 (mp) cc_final: 0.7547 (pt) REVERT: U 44 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6920 (pt0) REVERT: U 126 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6746 (tm-30) REVERT: W 8 PHE cc_start: 0.6114 (m-80) cc_final: 0.5452 (t80) REVERT: W 62 MET cc_start: 0.8301 (ttp) cc_final: 0.7966 (ttp) REVERT: X 12 LYS cc_start: 0.6724 (tppp) cc_final: 0.6341 (ttpt) REVERT: X 32 LYS cc_start: 0.8901 (tppt) cc_final: 0.8205 (ttpt) REVERT: X 78 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7067 (mmt-90) REVERT: X 88 LYS cc_start: 0.7564 (ttmm) cc_final: 0.6968 (tmtt) REVERT: X 111 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7156 (ptm) REVERT: X 112 ASP cc_start: 0.7470 (p0) cc_final: 0.7114 (p0) REVERT: Y 92 ASN cc_start: 0.6798 (p0) cc_final: 0.6556 (p0) REVERT: Y 93 PHE cc_start: 0.7563 (m-10) cc_final: 0.7353 (m-10) REVERT: Y 105 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6039 (m-80) outliers start: 175 outliers final: 116 residues processed: 862 average time/residue: 0.8283 time to fit residues: 1228.6204 Evaluate side-chains 818 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 688 time to evaluate : 5.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 31 TYR Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain g residue 141 CYS Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 197 GLN Chi-restraints excluded: chain H residue 218 LYS Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 41 ILE Chi-restraints excluded: chain h residue 91 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 196 ASN Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 153 LYS Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain x residue 633 CYS Chi-restraints excluded: chain x residue 652 THR Chi-restraints excluded: chain x residue 673 LEU Chi-restraints excluded: chain x residue 709 ASN Chi-restraints excluded: chain x residue 742 LEU Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 892 GLU Chi-restraints excluded: chain x residue 943 LEU Chi-restraints excluded: chain x residue 985 THR Chi-restraints excluded: chain x residue 999 SER Chi-restraints excluded: chain x residue 1031 VAL Chi-restraints excluded: chain x residue 1042 ASP Chi-restraints excluded: chain x residue 1059 ILE Chi-restraints excluded: chain x residue 1099 ILE Chi-restraints excluded: chain x residue 1118 LYS Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 87 GLU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 73 ASN Chi-restraints excluded: chain T residue 125 HIS Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 108 GLU Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain W residue 50 PHE Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain X residue 78 ARG Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 111 MET Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 105 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 601 optimal weight: 20.0000 chunk 409 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 537 optimal weight: 0.0030 chunk 297 optimal weight: 0.9980 chunk 616 optimal weight: 0.7980 chunk 499 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 368 optimal weight: 6.9990 chunk 648 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 overall best weight: 2.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 45 ASN B 9 GLN b 19 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 GLN x1062 HIS L 7 ASN L 61 GLN ** O 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN P 26 ASN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN T 101 ASN ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 93743 Z= 0.154 Angle : 0.525 11.380 136219 Z= 0.266 Chirality : 0.034 0.279 16874 Planarity : 0.004 0.054 9815 Dihedral : 22.632 179.422 37727 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.01 % Allowed : 20.33 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.02 (0.11), residues: 5551 helix: 0.64 (0.13), residues: 1707 sheet: -0.68 (0.17), residues: 924 loop : -1.51 (0.11), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP x1205 HIS 0.008 0.001 HIS x1025 PHE 0.022 0.001 PHE x1196 TYR 0.026 0.001 TYR B 156 ARG 0.008 0.000 ARG Z 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 724 time to evaluate : 5.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 72 PHE cc_start: 0.7384 (m-80) cc_final: 0.7159 (m-10) REVERT: Z 113 ARG cc_start: 0.8469 (mmm160) cc_final: 0.7965 (mtm-85) REVERT: A 46 ARG cc_start: 0.5170 (mtm180) cc_final: 0.4591 (ptp-170) REVERT: A 114 LYS cc_start: 0.3463 (mmtm) cc_final: 0.3231 (mttt) REVERT: a 52 LYS cc_start: 0.7495 (tptp) cc_final: 0.6759 (pttp) REVERT: a 78 LYS cc_start: 0.6647 (mttp) cc_final: 0.6206 (mmtm) REVERT: a 108 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8176 (mt) REVERT: a 112 ASN cc_start: 0.5481 (m110) cc_final: 0.4736 (p0) REVERT: B 80 ARG cc_start: 0.6940 (mmm-85) cc_final: 0.6263 (tpt170) REVERT: B 132 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6779 (tt0) REVERT: B 156 TYR cc_start: 0.8233 (m-80) cc_final: 0.7892 (m-80) REVERT: B 205 ARG cc_start: 0.5423 (OUTLIER) cc_final: 0.4609 (ptm160) REVERT: b 33 ASP cc_start: 0.8588 (p0) cc_final: 0.8239 (p0) REVERT: C 224 GLU cc_start: 0.6320 (pp20) cc_final: 0.5734 (mm-30) REVERT: D 105 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6348 (mp0) REVERT: D 108 LYS cc_start: 0.5779 (ttmt) cc_final: 0.5238 (ttpp) REVERT: D 215 MET cc_start: 0.7904 (ptp) cc_final: 0.7516 (ttp) REVERT: D 250 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.6996 (t80) REVERT: D 251 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8037 (mt) REVERT: d 10 LYS cc_start: 0.6606 (tttm) cc_final: 0.5967 (mttt) REVERT: E 17 PHE cc_start: 0.6289 (t80) cc_final: 0.5956 (t80) REVERT: E 40 ARG cc_start: 0.5851 (ttt180) cc_final: 0.5003 (mmt180) REVERT: e 12 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.6260 (mmp80) REVERT: F 66 MET cc_start: 0.6950 (ppp) cc_final: 0.6507 (ttt) REVERT: F 168 LYS cc_start: 0.7136 (mmmt) cc_final: 0.6688 (mttm) REVERT: f 86 ARG cc_start: 0.7754 (ttt90) cc_final: 0.7490 (ttm-80) REVERT: G 42 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7714 (mttp) REVERT: G 185 SER cc_start: 0.7704 (t) cc_final: 0.7417 (p) REVERT: H 32 MET cc_start: 0.8249 (mpp) cc_final: 0.7761 (mpp) REVERT: H 106 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7926 (tt) REVERT: H 217 MET cc_start: 0.6396 (tpp) cc_final: 0.5209 (ttt) REVERT: H 223 LYS cc_start: 0.5652 (mmpt) cc_final: 0.5352 (tptp) REVERT: h 29 ASP cc_start: 0.5443 (OUTLIER) cc_final: 0.4193 (t0) REVERT: h 139 LYS cc_start: 0.5603 (mmmm) cc_final: 0.5341 (ttmt) REVERT: h 217 MET cc_start: 0.3949 (ppp) cc_final: 0.3393 (ptm) REVERT: h 304 ASP cc_start: 0.7302 (t0) cc_final: 0.6644 (p0) REVERT: I 32 MET cc_start: 0.5208 (tpt) cc_final: 0.4872 (mtp) REVERT: I 37 LYS cc_start: 0.4727 (mmtm) cc_final: 0.4083 (pttt) REVERT: I 173 PHE cc_start: 0.7052 (m-80) cc_final: 0.6835 (m-80) REVERT: J 165 GLN cc_start: 0.6724 (pt0) cc_final: 0.5778 (mm-40) REVERT: n 21 ARG cc_start: 0.4948 (ttm170) cc_final: 0.4671 (ttp-110) REVERT: K 55 LYS cc_start: 0.6543 (ttmt) cc_final: 0.5974 (mttm) REVERT: K 66 LYS cc_start: 0.8350 (tttt) cc_final: 0.7928 (mttm) REVERT: K 75 ASN cc_start: 0.6419 (t0) cc_final: 0.5993 (t0) REVERT: K 79 ARG cc_start: 0.7388 (tpp80) cc_final: 0.6929 (mmp80) REVERT: K 117 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7747 (mm) REVERT: K 155 LYS cc_start: 0.7943 (mtpt) cc_final: 0.7741 (mmtp) REVERT: x 1006 ILE cc_start: 0.6454 (pt) cc_final: 0.5811 (mm) REVERT: x 1073 ASP cc_start: 0.6865 (m-30) cc_final: 0.6436 (t0) REVERT: x 1083 LYS cc_start: 0.6373 (tttt) cc_final: 0.6065 (pttm) REVERT: x 1206 GLN cc_start: 0.8464 (tp40) cc_final: 0.8213 (pt0) REVERT: L 1 MET cc_start: 0.4049 (OUTLIER) cc_final: 0.3592 (mmt) REVERT: L 27 VAL cc_start: 0.7425 (m) cc_final: 0.7152 (p) REVERT: M 5 GLN cc_start: 0.7470 (mp10) cc_final: 0.7009 (mp10) REVERT: M 7 GLU cc_start: 0.7957 (pm20) cc_final: 0.7518 (pm20) REVERT: M 67 SER cc_start: 0.8875 (t) cc_final: 0.8423 (m) REVERT: N 99 LYS cc_start: 0.3191 (pptt) cc_final: 0.2830 (pttm) REVERT: O 32 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.6578 (t0) REVERT: O 38 TYR cc_start: 0.6475 (m-80) cc_final: 0.6254 (m-80) REVERT: O 100 LYS cc_start: 0.8014 (tppt) cc_final: 0.7666 (tttm) REVERT: P 37 PHE cc_start: 0.8249 (m-80) cc_final: 0.7954 (m-10) REVERT: P 87 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5517 (pt0) REVERT: P 138 ASP cc_start: 0.5432 (OUTLIER) cc_final: 0.5168 (p0) REVERT: Q 28 MET cc_start: 0.5677 (OUTLIER) cc_final: 0.5221 (tmm) REVERT: Q 30 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.4832 (t80) REVERT: Q 59 ARG cc_start: 0.4690 (tmt-80) cc_final: 0.4134 (ttm170) REVERT: R 41 MET cc_start: 0.7596 (tpp) cc_final: 0.7218 (tpp) REVERT: R 42 ILE cc_start: 0.7956 (mm) cc_final: 0.7661 (mt) REVERT: R 114 GLN cc_start: 0.7686 (pp30) cc_final: 0.7437 (pp30) REVERT: R 116 ASP cc_start: 0.7752 (t70) cc_final: 0.7547 (m-30) REVERT: S 7 LYS cc_start: 0.6650 (pttt) cc_final: 0.6329 (pptt) REVERT: S 18 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6066 (mm-30) REVERT: S 94 GLU cc_start: 0.6892 (pm20) cc_final: 0.6606 (mp0) REVERT: S 98 VAL cc_start: 0.7106 (t) cc_final: 0.6717 (p) REVERT: T 14 ARG cc_start: 0.6712 (tpp80) cc_final: 0.6378 (tpp80) REVERT: T 19 ASN cc_start: 0.5724 (m-40) cc_final: 0.5148 (p0) REVERT: T 73 ASN cc_start: 0.7378 (p0) cc_final: 0.7120 (p0) REVERT: T 83 PHE cc_start: 0.6441 (t80) cc_final: 0.5935 (t80) REVERT: T 127 TRP cc_start: 0.7291 (m-10) cc_final: 0.7036 (m100) REVERT: T 134 GLN cc_start: 0.6204 (mm110) cc_final: 0.5490 (mm-40) REVERT: T 144 ARG cc_start: 0.4621 (ptt180) cc_final: 0.3745 (ptp-170) REVERT: U 5 THR cc_start: 0.7033 (t) cc_final: 0.6713 (p) REVERT: U 28 LEU cc_start: 0.7777 (mp) cc_final: 0.7514 (pt) REVERT: U 35 ASP cc_start: 0.6359 (OUTLIER) cc_final: 0.5969 (t0) REVERT: U 44 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6843 (pt0) REVERT: U 105 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6811 (mm-40) REVERT: U 126 GLN cc_start: 0.7321 (mm-40) cc_final: 0.6749 (tm-30) REVERT: W 8 PHE cc_start: 0.6137 (m-80) cc_final: 0.5469 (t80) REVERT: W 64 GLU cc_start: 0.8014 (pm20) cc_final: 0.7740 (pm20) REVERT: X 12 LYS cc_start: 0.6725 (tppp) cc_final: 0.6310 (ttpt) REVERT: X 32 LYS cc_start: 0.8920 (tppt) cc_final: 0.8231 (ttpt) REVERT: X 88 LYS cc_start: 0.7523 (ttmm) cc_final: 0.6934 (tmtt) REVERT: X 111 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7175 (ptm) REVERT: X 112 ASP cc_start: 0.7373 (p0) cc_final: 0.7113 (p0) REVERT: Y 71 ARG cc_start: 0.5763 (ttm-80) cc_final: 0.5554 (tpp80) REVERT: Y 105 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.5988 (m-80) outliers start: 195 outliers final: 135 residues processed: 854 average time/residue: 0.9037 time to fit residues: 1334.8229 Evaluate side-chains 837 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 683 time to evaluate : 5.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 108 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 31 TYR Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain g residue 141 CYS Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 197 GLN Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 29 ASP Chi-restraints excluded: chain h residue 40 ILE Chi-restraints excluded: chain h residue 41 ILE Chi-restraints excluded: chain h residue 91 ASP Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 196 ASN Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 153 LYS Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain x residue 633 CYS Chi-restraints excluded: chain x residue 652 THR Chi-restraints excluded: chain x residue 673 LEU Chi-restraints excluded: chain x residue 709 ASN Chi-restraints excluded: chain x residue 742 LEU Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 794 VAL Chi-restraints excluded: chain x residue 892 GLU Chi-restraints excluded: chain x residue 999 SER Chi-restraints excluded: chain x residue 1028 GLN Chi-restraints excluded: chain x residue 1042 ASP Chi-restraints excluded: chain x residue 1092 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 87 GLU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain T residue 125 HIS Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain U residue 108 GLU Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 111 MET Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 105 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 242 optimal weight: 9.9990 chunk 650 optimal weight: 40.0000 chunk 142 optimal weight: 20.0000 chunk 423 optimal weight: 0.1980 chunk 178 optimal weight: 5.9990 chunk 722 optimal weight: 3.9990 chunk 599 optimal weight: 5.9990 chunk 334 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 379 optimal weight: 9.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 45 ASN B 9 GLN b 19 GLN C 232 HIS D 113 GLN e 37 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 HIS x1062 HIS O 36 GLN O 62 GLN P 26 ASN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 GLN X 92 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 93743 Z= 0.277 Angle : 0.645 14.458 136219 Z= 0.325 Chirality : 0.039 0.280 16874 Planarity : 0.005 0.053 9815 Dihedral : 22.735 179.894 37727 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.94 % Allowed : 20.83 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.28 (0.11), residues: 5551 helix: 0.46 (0.13), residues: 1700 sheet: -1.03 (0.17), residues: 918 loop : -1.61 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP e 8 HIS 0.009 0.001 HIS x1025 PHE 0.059 0.002 PHE x 806 TYR 0.030 0.002 TYR B 156 ARG 0.009 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 712 time to evaluate : 5.232 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: A 46 ARG cc_start: 0.5079 (mtm180) cc_final: 0.4480 (ptp-170) REVERT: A 67 LYS cc_start: 0.6119 (mmtp) cc_final: 0.5903 (tmtt) REVERT: A 114 LYS cc_start: 0.3480 (mmtm) cc_final: 0.3235 (mttt) REVERT: a 52 LYS cc_start: 0.7472 (tptp) cc_final: 0.6780 (pttp) REVERT: a 78 LYS cc_start: 0.6733 (mttp) cc_final: 0.6239 (mmtm) REVERT: a 94 LYS cc_start: 0.5577 (tmmt) cc_final: 0.5253 (mmtp) REVERT: a 112 ASN cc_start: 0.5432 (m110) cc_final: 0.4707 (p0) REVERT: B 80 ARG cc_start: 0.7002 (mmm-85) cc_final: 0.6714 (mmm160) REVERT: B 104 THR cc_start: 0.6816 (t) cc_final: 0.6594 (t) REVERT: B 132 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: b 33 ASP cc_start: 0.8471 (p0) cc_final: 0.7726 (p0) REVERT: b 85 ARG cc_start: 0.5828 (mtp85) cc_final: 0.5556 (mtp-110) REVERT: C 224 GLU cc_start: 0.6305 (pp20) cc_final: 0.5557 (mm-30) REVERT: D 105 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: D 108 LYS cc_start: 0.5817 (ttmt) cc_final: 0.5289 (ttpp) REVERT: D 215 MET cc_start: 0.7861 (ptp) cc_final: 0.7561 (ttp) REVERT: D 250 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.7051 (t80) REVERT: d 10 LYS cc_start: 0.6645 (tttm) cc_final: 0.5981 (mttt) REVERT: E 17 PHE cc_start: 0.6304 (t80) cc_final: 0.5911 (t80) REVERT: E 40 ARG cc_start: 0.5817 (ttt180) cc_final: 0.5039 (mmt180) REVERT: E 212 GLU cc_start: 0.4444 (pp20) cc_final: 0.4232 (mt-10) REVERT: e 12 ARG cc_start: 0.6560 (mpt180) cc_final: 0.5983 (mmp80) REVERT: e 27 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7100 (ptp-110) REVERT: F 66 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.6336 (ttt) REVERT: F 168 LYS cc_start: 0.7214 (mmmt) cc_final: 0.6610 (mttp) REVERT: f 109 MET cc_start: 0.5074 (OUTLIER) cc_final: 0.4791 (tmm) REVERT: G 42 LYS cc_start: 0.7965 (mtpt) cc_final: 0.7691 (mttm) REVERT: G 185 SER cc_start: 0.7963 (t) cc_final: 0.7712 (p) REVERT: H 217 MET cc_start: 0.6388 (tpp) cc_final: 0.5166 (ttt) REVERT: h 17 TRP cc_start: 0.4265 (OUTLIER) cc_final: 0.4030 (p90) REVERT: h 304 ASP cc_start: 0.7246 (t0) cc_final: 0.6618 (p0) REVERT: I 32 MET cc_start: 0.5181 (tpt) cc_final: 0.4829 (mtp) REVERT: I 37 LYS cc_start: 0.4608 (mmtm) cc_final: 0.3948 (pttt) REVERT: I 115 LYS cc_start: 0.6385 (tttp) cc_final: 0.5896 (ttmt) REVERT: J 165 GLN cc_start: 0.6670 (pt0) cc_final: 0.5661 (mm-40) REVERT: n 21 ARG cc_start: 0.5248 (ttm170) cc_final: 0.4692 (ttp-110) REVERT: K 55 LYS cc_start: 0.6575 (ttmt) cc_final: 0.6053 (mttm) REVERT: K 66 LYS cc_start: 0.8237 (tttt) cc_final: 0.7819 (mmtm) REVERT: K 79 ARG cc_start: 0.7486 (tpp80) cc_final: 0.6903 (mmp80) REVERT: K 117 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7415 (mm) REVERT: K 155 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7713 (mmtp) REVERT: x 909 LYS cc_start: 0.4567 (pttp) cc_final: 0.3577 (mtmt) REVERT: x 1006 ILE cc_start: 0.6578 (pt) cc_final: 0.5990 (mm) REVERT: x 1038 ARG cc_start: 0.6313 (ptt180) cc_final: 0.5670 (ptm-80) REVERT: x 1073 ASP cc_start: 0.6881 (m-30) cc_final: 0.6412 (t0) REVERT: x 1083 LYS cc_start: 0.6363 (tttt) cc_final: 0.6020 (pttt) REVERT: x 1178 ASP cc_start: 0.3258 (t70) cc_final: 0.2409 (p0) REVERT: x 1206 GLN cc_start: 0.8451 (tp40) cc_final: 0.8188 (pt0) REVERT: L 27 VAL cc_start: 0.7575 (m) cc_final: 0.7324 (p) REVERT: M 5 GLN cc_start: 0.7362 (mp10) cc_final: 0.7069 (mp10) REVERT: M 7 GLU cc_start: 0.8002 (pm20) cc_final: 0.7485 (pm20) REVERT: M 67 SER cc_start: 0.8941 (t) cc_final: 0.8548 (m) REVERT: N 99 LYS cc_start: 0.3368 (pptt) cc_final: 0.3063 (pttm) REVERT: O 32 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.6836 (t0) REVERT: O 100 LYS cc_start: 0.8206 (tppt) cc_final: 0.7949 (tttm) REVERT: P 37 PHE cc_start: 0.8213 (m-80) cc_final: 0.7951 (m-10) REVERT: P 87 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5575 (pt0) REVERT: P 103 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7017 (p0) REVERT: P 138 ASP cc_start: 0.5479 (OUTLIER) cc_final: 0.5206 (p0) REVERT: Q 28 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5375 (tmm) REVERT: Q 30 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.5083 (t80) REVERT: R 41 MET cc_start: 0.7590 (tpp) cc_final: 0.7277 (tpp) REVERT: R 42 ILE cc_start: 0.8017 (mm) cc_final: 0.7619 (tp) REVERT: S 7 LYS cc_start: 0.6730 (pttt) cc_final: 0.6411 (pptt) REVERT: S 98 VAL cc_start: 0.6727 (t) cc_final: 0.6164 (p) REVERT: T 19 ASN cc_start: 0.6060 (m-40) cc_final: 0.5717 (p0) REVERT: T 71 MET cc_start: 0.7165 (tmm) cc_final: 0.6759 (tmm) REVERT: T 83 PHE cc_start: 0.6580 (t80) cc_final: 0.6088 (t80) REVERT: T 127 TRP cc_start: 0.7198 (m-10) cc_final: 0.6974 (m100) REVERT: T 134 GLN cc_start: 0.6081 (mm110) cc_final: 0.5386 (mm-40) REVERT: U 5 THR cc_start: 0.6911 (t) cc_final: 0.6591 (p) REVERT: U 28 LEU cc_start: 0.7746 (mp) cc_final: 0.7472 (pt) REVERT: U 35 ASP cc_start: 0.6520 (OUTLIER) cc_final: 0.6122 (t0) REVERT: U 83 GLN cc_start: 0.6050 (OUTLIER) cc_final: 0.4958 (mt0) REVERT: V 48 LEU cc_start: 0.3686 (OUTLIER) cc_final: 0.3274 (tt) REVERT: W 64 GLU cc_start: 0.8122 (pm20) cc_final: 0.7828 (pm20) REVERT: X 32 LYS cc_start: 0.8920 (tppt) cc_final: 0.8178 (ttpt) REVERT: X 78 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6783 (mmm-85) REVERT: X 88 LYS cc_start: 0.7496 (ttmm) cc_final: 0.6852 (tmtt) REVERT: Y 71 ARG cc_start: 0.5712 (ttm-80) cc_final: 0.5420 (tpp80) REVERT: Y 93 PHE cc_start: 0.7533 (m-10) cc_final: 0.7182 (m-10) REVERT: Y 105 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: Y 127 ASN cc_start: 0.8350 (m110) cc_final: 0.7997 (t0) outliers start: 240 outliers final: 168 residues processed: 877 average time/residue: 0.8151 time to fit residues: 1234.3050 Evaluate side-chains 848 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 662 time to evaluate : 5.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 31 TYR Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 132 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain g residue 141 CYS Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 197 GLN Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 29 ASP Chi-restraints excluded: chain h residue 40 ILE Chi-restraints excluded: chain h residue 41 ILE Chi-restraints excluded: chain h residue 91 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 196 ASN Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 252 THR Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 153 LYS Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain x residue 652 THR Chi-restraints excluded: chain x residue 671 VAL Chi-restraints excluded: chain x residue 673 LEU Chi-restraints excluded: chain x residue 709 ASN Chi-restraints excluded: chain x residue 742 LEU Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 858 VAL Chi-restraints excluded: chain x residue 884 ASP Chi-restraints excluded: chain x residue 895 ILE Chi-restraints excluded: chain x residue 985 THR Chi-restraints excluded: chain x residue 999 SER Chi-restraints excluded: chain x residue 1028 GLN Chi-restraints excluded: chain x residue 1031 VAL Chi-restraints excluded: chain x residue 1042 ASP Chi-restraints excluded: chain x residue 1099 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 87 GLU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 125 HIS Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 83 GLN Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain U residue 108 GLU Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 78 ARG Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 129 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 696 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 411 optimal weight: 5.9990 chunk 527 optimal weight: 1.9990 chunk 408 optimal weight: 4.9990 chunk 608 optimal weight: 0.0570 chunk 403 optimal weight: 30.0000 chunk 719 optimal weight: 5.9990 chunk 450 optimal weight: 20.0000 chunk 438 optimal weight: 6.9990 chunk 332 optimal weight: 10.0000 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 85 ASN a 45 ASN B 131 HIS b 19 GLN D 113 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 93743 Z= 0.204 Angle : 0.572 13.338 136219 Z= 0.289 Chirality : 0.036 0.277 16874 Planarity : 0.004 0.135 9815 Dihedral : 22.663 179.070 37727 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.63 % Allowed : 21.82 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.18 (0.11), residues: 5551 helix: 0.58 (0.13), residues: 1709 sheet: -0.97 (0.16), residues: 931 loop : -1.57 (0.11), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP h 17 HIS 0.008 0.001 HIS x1025 PHE 0.038 0.002 PHE K 115 TYR 0.031 0.001 TYR B 156 ARG 0.031 0.001 ARG x 614 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 712 time to evaluate : 5.408 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: Z 113 ARG cc_start: 0.8451 (mmm160) cc_final: 0.7973 (mtm-85) REVERT: A 46 ARG cc_start: 0.5011 (mtm180) cc_final: 0.4419 (ptp-170) REVERT: A 114 LYS cc_start: 0.3456 (mmtm) cc_final: 0.3198 (mttt) REVERT: a 52 LYS cc_start: 0.7423 (tptp) cc_final: 0.6701 (pttp) REVERT: a 78 LYS cc_start: 0.6617 (mttp) cc_final: 0.6136 (mmtm) REVERT: a 112 ASN cc_start: 0.5168 (m110) cc_final: 0.4419 (p0) REVERT: B 80 ARG cc_start: 0.7032 (mmm-85) cc_final: 0.6766 (mmm160) REVERT: B 104 THR cc_start: 0.6825 (t) cc_final: 0.6617 (t) REVERT: B 132 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6970 (mt0) REVERT: B 156 TYR cc_start: 0.8301 (m-80) cc_final: 0.8030 (m-80) REVERT: B 205 ARG cc_start: 0.5254 (OUTLIER) cc_final: 0.4864 (ptm160) REVERT: b 33 ASP cc_start: 0.8447 (p0) cc_final: 0.7646 (p0) REVERT: D 79 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6191 (pt0) REVERT: D 105 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6374 (mp0) REVERT: D 108 LYS cc_start: 0.5719 (ttmt) cc_final: 0.4972 (ttpp) REVERT: D 120 GLN cc_start: 0.6691 (pt0) cc_final: 0.6126 (pt0) REVERT: D 215 MET cc_start: 0.7807 (ptp) cc_final: 0.7492 (ttp) REVERT: D 249 SER cc_start: 0.9064 (m) cc_final: 0.8686 (p) REVERT: D 250 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6755 (t80) REVERT: d 10 LYS cc_start: 0.6702 (tttm) cc_final: 0.6004 (mttt) REVERT: E 17 PHE cc_start: 0.6327 (t80) cc_final: 0.5929 (t80) REVERT: E 40 ARG cc_start: 0.5909 (ttt180) cc_final: 0.5141 (mmt180) REVERT: e 12 ARG cc_start: 0.6463 (mpt180) cc_final: 0.5914 (mmp80) REVERT: F 168 LYS cc_start: 0.7202 (mmmt) cc_final: 0.6552 (mttp) REVERT: f 109 MET cc_start: 0.4978 (OUTLIER) cc_final: 0.4679 (tmm) REVERT: G 42 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7717 (mmtt) REVERT: G 185 SER cc_start: 0.8048 (t) cc_final: 0.7800 (p) REVERT: H 32 MET cc_start: 0.8242 (mpp) cc_final: 0.7841 (mpp) REVERT: H 217 MET cc_start: 0.6322 (tpp) cc_final: 0.5159 (ttt) REVERT: h 17 TRP cc_start: 0.4136 (OUTLIER) cc_final: 0.3830 (p90) REVERT: h 304 ASP cc_start: 0.7276 (t0) cc_final: 0.6629 (p0) REVERT: I 32 MET cc_start: 0.5237 (tpt) cc_final: 0.4862 (mtp) REVERT: I 37 LYS cc_start: 0.4701 (mmtm) cc_final: 0.4087 (pttt) REVERT: J 77 ARG cc_start: 0.6849 (ttm110) cc_final: 0.6616 (ttm110) REVERT: J 165 GLN cc_start: 0.6631 (pt0) cc_final: 0.5653 (mm-40) REVERT: n 21 ARG cc_start: 0.5153 (ttm170) cc_final: 0.4658 (ttp-110) REVERT: K 55 LYS cc_start: 0.6572 (ttmt) cc_final: 0.6056 (mttm) REVERT: K 66 LYS cc_start: 0.8256 (tttt) cc_final: 0.7782 (mmtm) REVERT: K 75 ASN cc_start: 0.6507 (t0) cc_final: 0.6077 (t0) REVERT: K 79 ARG cc_start: 0.7522 (tpp80) cc_final: 0.7018 (mmp80) REVERT: K 155 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7744 (mmtp) REVERT: x 921 LYS cc_start: 0.7575 (tptp) cc_final: 0.7006 (tmmt) REVERT: x 1006 ILE cc_start: 0.6475 (pt) cc_final: 0.5836 (mm) REVERT: x 1073 ASP cc_start: 0.6908 (m-30) cc_final: 0.6378 (t0) REVERT: x 1083 LYS cc_start: 0.6444 (tttt) cc_final: 0.6078 (pttm) REVERT: x 1178 ASP cc_start: 0.3663 (t70) cc_final: 0.2844 (p0) REVERT: x 1206 GLN cc_start: 0.8462 (tp40) cc_final: 0.8205 (pt0) REVERT: L 1 MET cc_start: 0.4227 (OUTLIER) cc_final: 0.3678 (mmt) REVERT: L 27 VAL cc_start: 0.7590 (m) cc_final: 0.7341 (p) REVERT: M 5 GLN cc_start: 0.7315 (mp10) cc_final: 0.7030 (mp10) REVERT: M 7 GLU cc_start: 0.8025 (pm20) cc_final: 0.7519 (pm20) REVERT: M 67 SER cc_start: 0.8913 (t) cc_final: 0.8480 (m) REVERT: N 99 LYS cc_start: 0.3491 (pptt) cc_final: 0.3203 (pttm) REVERT: O 32 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.6541 (t0) REVERT: O 100 LYS cc_start: 0.8279 (tppt) cc_final: 0.8013 (tttm) REVERT: P 37 PHE cc_start: 0.8237 (m-80) cc_final: 0.7975 (m-10) REVERT: P 87 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5572 (pt0) REVERT: P 138 ASP cc_start: 0.5504 (OUTLIER) cc_final: 0.5180 (p0) REVERT: Q 28 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.5297 (tmm) REVERT: Q 30 TYR cc_start: 0.6509 (OUTLIER) cc_final: 0.5038 (t80) REVERT: R 42 ILE cc_start: 0.8015 (mm) cc_final: 0.7575 (tp) REVERT: R 114 GLN cc_start: 0.7694 (pp30) cc_final: 0.7440 (pp30) REVERT: R 116 ASP cc_start: 0.8107 (m-30) cc_final: 0.7827 (m-30) REVERT: S 7 LYS cc_start: 0.6757 (pttt) cc_final: 0.6441 (pptt) REVERT: S 18 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6175 (mm-30) REVERT: S 24 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7359 (mm) REVERT: T 134 GLN cc_start: 0.6087 (mm110) cc_final: 0.5412 (mm-40) REVERT: U 5 THR cc_start: 0.6928 (t) cc_final: 0.6629 (p) REVERT: U 28 LEU cc_start: 0.7774 (mp) cc_final: 0.7508 (tp) REVERT: U 35 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.6021 (t0) REVERT: U 83 GLN cc_start: 0.6085 (OUTLIER) cc_final: 0.4945 (mt0) REVERT: W 64 GLU cc_start: 0.8137 (pm20) cc_final: 0.7929 (pm20) REVERT: X 32 LYS cc_start: 0.8894 (tppt) cc_final: 0.8175 (ttpt) REVERT: X 78 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6419 (mmm-85) REVERT: X 88 LYS cc_start: 0.7491 (ttmm) cc_final: 0.6867 (tmtt) REVERT: Y 93 PHE cc_start: 0.7542 (m-10) cc_final: 0.7217 (m-10) REVERT: Y 105 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.5886 (m-80) REVERT: Y 127 ASN cc_start: 0.8354 (m110) cc_final: 0.8021 (t0) outliers start: 225 outliers final: 161 residues processed: 868 average time/residue: 0.8144 time to fit residues: 1218.7265 Evaluate side-chains 856 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 677 time to evaluate : 5.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 74 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain c residue 31 TYR Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 57 VAL Chi-restraints excluded: chain c residue 75 GLU Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 132 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 197 GLN Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 29 ASP Chi-restraints excluded: chain h residue 40 ILE Chi-restraints excluded: chain h residue 41 ILE Chi-restraints excluded: chain h residue 91 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 196 ASN Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 252 THR Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 153 LYS Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain x residue 633 CYS Chi-restraints excluded: chain x residue 651 HIS Chi-restraints excluded: chain x residue 652 THR Chi-restraints excluded: chain x residue 671 VAL Chi-restraints excluded: chain x residue 673 LEU Chi-restraints excluded: chain x residue 709 ASN Chi-restraints excluded: chain x residue 742 LEU Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 908 MET Chi-restraints excluded: chain x residue 945 LEU Chi-restraints excluded: chain x residue 999 SER Chi-restraints excluded: chain x residue 1014 LYS Chi-restraints excluded: chain x residue 1028 GLN Chi-restraints excluded: chain x residue 1031 VAL Chi-restraints excluded: chain x residue 1042 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 87 GLU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 125 HIS Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 83 GLN Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 78 ARG Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 129 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 445 optimal weight: 40.0000 chunk 287 optimal weight: 8.9990 chunk 430 optimal weight: 20.0000 chunk 216 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 457 optimal weight: 6.9990 chunk 490 optimal weight: 6.9990 chunk 355 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 565 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 45 ASN B 9 GLN b 19 GLN c 9 HIS D 113 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN h 14 HIS O 62 GLN P 26 ASN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 142 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN T 101 ASN ** U 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 ASN Y 77 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 93743 Z= 0.296 Angle : 0.665 15.526 136219 Z= 0.335 Chirality : 0.039 0.291 16874 Planarity : 0.005 0.057 9815 Dihedral : 22.769 179.269 37727 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.02 % Favored : 91.97 % Rotamer: Outliers : 5.12 % Allowed : 22.02 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.43 (0.11), residues: 5551 helix: 0.37 (0.13), residues: 1704 sheet: -1.19 (0.16), residues: 907 loop : -1.69 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP h 17 HIS 0.009 0.001 HIS x1025 PHE 0.025 0.002 PHE x1196 TYR 0.033 0.002 TYR B 156 ARG 0.007 0.001 ARG H 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 687 time to evaluate : 5.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.5114 (mtm180) cc_final: 0.4554 (ptp-170) REVERT: A 111 GLU cc_start: 0.5412 (OUTLIER) cc_final: 0.5045 (pm20) REVERT: A 114 LYS cc_start: 0.3473 (mmtm) cc_final: 0.3255 (mttt) REVERT: a 52 LYS cc_start: 0.7338 (tptp) cc_final: 0.6636 (pttp) REVERT: a 78 LYS cc_start: 0.6690 (mttp) cc_final: 0.6236 (mmtm) REVERT: B 80 ARG cc_start: 0.7011 (mmm-85) cc_final: 0.6750 (mmm160) REVERT: B 104 THR cc_start: 0.6843 (t) cc_final: 0.6616 (t) REVERT: B 128 ARG cc_start: 0.7556 (tpp-160) cc_final: 0.6865 (mmm160) REVERT: B 132 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7046 (mt0) REVERT: B 156 TYR cc_start: 0.8364 (m-80) cc_final: 0.8030 (m-80) REVERT: B 205 ARG cc_start: 0.5237 (OUTLIER) cc_final: 0.4871 (ptm160) REVERT: b 33 ASP cc_start: 0.8418 (p0) cc_final: 0.7647 (p0) REVERT: b 85 ARG cc_start: 0.5928 (mtp85) cc_final: 0.5596 (mtp-110) REVERT: C 224 GLU cc_start: 0.5866 (pp20) cc_final: 0.5054 (tp30) REVERT: c 15 GLU cc_start: 0.7271 (tp30) cc_final: 0.6779 (tp30) REVERT: D 105 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: D 108 LYS cc_start: 0.5820 (ttmt) cc_final: 0.5270 (ttpp) REVERT: D 120 GLN cc_start: 0.6829 (pt0) cc_final: 0.6249 (pt0) REVERT: D 250 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6829 (t80) REVERT: d 10 LYS cc_start: 0.6640 (tttm) cc_final: 0.5975 (mttt) REVERT: d 40 ARG cc_start: 0.4926 (OUTLIER) cc_final: 0.4570 (ptm160) REVERT: E 40 ARG cc_start: 0.5892 (ttt180) cc_final: 0.5087 (mmt180) REVERT: E 127 MET cc_start: 0.7680 (mmm) cc_final: 0.7309 (mmm) REVERT: e 12 ARG cc_start: 0.6363 (mpt180) cc_final: 0.5885 (mmp80) REVERT: e 27 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7079 (ptp-110) REVERT: f 109 MET cc_start: 0.4941 (OUTLIER) cc_final: 0.4652 (tmm) REVERT: G 42 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7727 (mmtt) REVERT: G 171 GLU cc_start: 0.7830 (pp20) cc_final: 0.7325 (tm-30) REVERT: G 185 SER cc_start: 0.8142 (t) cc_final: 0.7888 (p) REVERT: H 217 MET cc_start: 0.6282 (tpp) cc_final: 0.5154 (ttt) REVERT: h 17 TRP cc_start: 0.4409 (OUTLIER) cc_final: 0.3998 (p-90) REVERT: h 183 LYS cc_start: 0.6960 (tmtt) cc_final: 0.6255 (mptt) REVERT: h 304 ASP cc_start: 0.7208 (t0) cc_final: 0.6567 (p0) REVERT: I 32 MET cc_start: 0.5221 (tpt) cc_final: 0.4823 (mtp) REVERT: I 37 LYS cc_start: 0.4621 (mmtm) cc_final: 0.3954 (pttt) REVERT: I 115 LYS cc_start: 0.6399 (tttp) cc_final: 0.5903 (ttmt) REVERT: I 173 PHE cc_start: 0.7315 (m-80) cc_final: 0.6968 (m-80) REVERT: J 79 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7721 (mp) REVERT: J 165 GLN cc_start: 0.6658 (pt0) cc_final: 0.5620 (mm-40) REVERT: n 21 ARG cc_start: 0.5235 (ttm170) cc_final: 0.4750 (ttp-110) REVERT: K 55 LYS cc_start: 0.6651 (ttmt) cc_final: 0.6167 (mttm) REVERT: K 66 LYS cc_start: 0.8215 (tttt) cc_final: 0.7765 (mmtm) REVERT: K 79 ARG cc_start: 0.7480 (tpp80) cc_final: 0.6955 (mmp80) REVERT: K 117 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7412 (mm) REVERT: K 155 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7697 (mmtp) REVERT: x 651 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.6838 (m-70) REVERT: x 796 PHE cc_start: 0.7638 (m-80) cc_final: 0.7338 (t80) REVERT: x 909 LYS cc_start: 0.4709 (pttp) cc_final: 0.3642 (mttt) REVERT: x 921 LYS cc_start: 0.7517 (tptp) cc_final: 0.7043 (tmmt) REVERT: x 1006 ILE cc_start: 0.6658 (pt) cc_final: 0.6087 (mm) REVERT: x 1029 TYR cc_start: 0.4508 (p90) cc_final: 0.4287 (p90) REVERT: x 1038 ARG cc_start: 0.6408 (ptt180) cc_final: 0.5745 (ptm-80) REVERT: x 1044 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.6474 (tm-30) REVERT: x 1073 ASP cc_start: 0.6890 (m-30) cc_final: 0.6262 (t0) REVERT: x 1083 LYS cc_start: 0.6300 (tttt) cc_final: 0.5907 (pttm) REVERT: x 1178 ASP cc_start: 0.3752 (t70) cc_final: 0.3089 (p0) REVERT: x 1206 GLN cc_start: 0.8382 (tp40) cc_final: 0.8131 (pt0) REVERT: L 27 VAL cc_start: 0.7592 (m) cc_final: 0.7345 (p) REVERT: M 5 GLN cc_start: 0.7200 (mp10) cc_final: 0.6781 (mp10) REVERT: M 7 GLU cc_start: 0.8017 (pm20) cc_final: 0.7469 (pm20) REVERT: M 67 SER cc_start: 0.8904 (t) cc_final: 0.8562 (m) REVERT: N 99 LYS cc_start: 0.3483 (pptt) cc_final: 0.3230 (pttm) REVERT: O 32 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7067 (t0) REVERT: O 100 LYS cc_start: 0.8256 (tppt) cc_final: 0.8040 (tttm) REVERT: P 37 PHE cc_start: 0.8322 (m-80) cc_final: 0.8104 (m-10) REVERT: P 87 GLU cc_start: 0.6112 (OUTLIER) cc_final: 0.5491 (pt0) REVERT: P 138 ASP cc_start: 0.5492 (OUTLIER) cc_final: 0.5209 (p0) REVERT: Q 28 MET cc_start: 0.5512 (OUTLIER) cc_final: 0.5234 (tmm) REVERT: Q 30 TYR cc_start: 0.6476 (OUTLIER) cc_final: 0.5231 (t80) REVERT: R 42 ILE cc_start: 0.8100 (mm) cc_final: 0.7603 (tp) REVERT: S 24 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7262 (mm) REVERT: T 83 PHE cc_start: 0.6502 (t80) cc_final: 0.6074 (t80) REVERT: T 134 GLN cc_start: 0.5992 (mm110) cc_final: 0.5381 (mm-40) REVERT: U 5 THR cc_start: 0.6848 (t) cc_final: 0.6590 (p) REVERT: U 28 LEU cc_start: 0.7728 (mp) cc_final: 0.7477 (tp) REVERT: U 35 ASP cc_start: 0.6465 (OUTLIER) cc_final: 0.6094 (t0) REVERT: U 83 GLN cc_start: 0.6135 (OUTLIER) cc_final: 0.5070 (mt0) REVERT: V 48 LEU cc_start: 0.3665 (OUTLIER) cc_final: 0.3078 (tt) REVERT: W 33 GLN cc_start: 0.8202 (tp40) cc_final: 0.7880 (tp40) REVERT: X 32 LYS cc_start: 0.8913 (tppt) cc_final: 0.8189 (ttpt) REVERT: X 78 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6651 (mmm-85) REVERT: X 88 LYS cc_start: 0.7456 (ttmm) cc_final: 0.6982 (tmtt) REVERT: Y 93 PHE cc_start: 0.7563 (m-10) cc_final: 0.7264 (m-10) REVERT: Y 105 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6149 (m-80) REVERT: Y 127 ASN cc_start: 0.8328 (m110) cc_final: 0.7980 (t0) outliers start: 249 outliers final: 191 residues processed: 863 average time/residue: 0.8328 time to fit residues: 1228.0509 Evaluate side-chains 867 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 653 time to evaluate : 5.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 74 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 31 TYR Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 75 GLU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 132 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 197 GLN Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 29 ASP Chi-restraints excluded: chain h residue 41 ILE Chi-restraints excluded: chain h residue 91 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 196 ASN Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 252 THR Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 153 LYS Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain x residue 633 CYS Chi-restraints excluded: chain x residue 651 HIS Chi-restraints excluded: chain x residue 652 THR Chi-restraints excluded: chain x residue 673 LEU Chi-restraints excluded: chain x residue 709 ASN Chi-restraints excluded: chain x residue 742 LEU Chi-restraints excluded: chain x residue 747 CYS Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 858 VAL Chi-restraints excluded: chain x residue 884 ASP Chi-restraints excluded: chain x residue 895 ILE Chi-restraints excluded: chain x residue 945 LEU Chi-restraints excluded: chain x residue 985 THR Chi-restraints excluded: chain x residue 999 SER Chi-restraints excluded: chain x residue 1014 LYS Chi-restraints excluded: chain x residue 1028 GLN Chi-restraints excluded: chain x residue 1031 VAL Chi-restraints excluded: chain x residue 1042 ASP Chi-restraints excluded: chain x residue 1044 GLN Chi-restraints excluded: chain x residue 1100 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 29 MET Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 87 GLU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 73 ASN Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 83 GLN Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 78 ARG Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 129 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 654 optimal weight: 9.9990 chunk 689 optimal weight: 9.9990 chunk 629 optimal weight: 7.9990 chunk 670 optimal weight: 9.9990 chunk 403 optimal weight: 8.9990 chunk 292 optimal weight: 8.9990 chunk 526 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 606 optimal weight: 0.8980 chunk 634 optimal weight: 0.9980 chunk 668 optimal weight: 8.9990 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 45 ASN b 19 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 142 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN T 101 ASN ** U 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 93743 Z= 0.253 Angle : 0.623 14.734 136219 Z= 0.314 Chirality : 0.038 0.276 16874 Planarity : 0.005 0.066 9815 Dihedral : 22.743 178.974 37727 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.03 % Favored : 93.95 % Rotamer: Outliers : 4.82 % Allowed : 22.74 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.42 (0.11), residues: 5551 helix: 0.40 (0.13), residues: 1699 sheet: -1.15 (0.16), residues: 908 loop : -1.72 (0.11), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP h 17 HIS 0.008 0.001 HIS x1025 PHE 0.037 0.002 PHE h 65 TYR 0.029 0.002 TYR B 156 ARG 0.013 0.001 ARG Z 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 673 time to evaluate : 5.340 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: Z 113 ARG cc_start: 0.8489 (mmm160) cc_final: 0.8071 (mtm-85) REVERT: A 46 ARG cc_start: 0.5144 (mtm180) cc_final: 0.4505 (ptp-170) REVERT: A 111 GLU cc_start: 0.5357 (OUTLIER) cc_final: 0.5006 (pm20) REVERT: A 114 LYS cc_start: 0.3507 (mmtm) cc_final: 0.3270 (mttt) REVERT: a 52 LYS cc_start: 0.7425 (tptp) cc_final: 0.6679 (pttp) REVERT: a 78 LYS cc_start: 0.6700 (mttp) cc_final: 0.6258 (mmtm) REVERT: B 80 ARG cc_start: 0.7002 (mmm-85) cc_final: 0.6754 (mmm160) REVERT: B 104 THR cc_start: 0.6828 (t) cc_final: 0.6603 (t) REVERT: B 128 ARG cc_start: 0.7531 (tpp-160) cc_final: 0.6868 (mmm160) REVERT: B 132 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6999 (mt0) REVERT: B 205 ARG cc_start: 0.5147 (OUTLIER) cc_final: 0.4835 (ptm160) REVERT: b 33 ASP cc_start: 0.8410 (p0) cc_final: 0.7649 (p0) REVERT: C 224 GLU cc_start: 0.5751 (pp20) cc_final: 0.4806 (tp30) REVERT: c 15 GLU cc_start: 0.7245 (tp30) cc_final: 0.6755 (tp30) REVERT: D 72 ASP cc_start: 0.5810 (t70) cc_final: 0.5233 (t70) REVERT: D 105 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: D 108 LYS cc_start: 0.5812 (ttmt) cc_final: 0.5270 (ttpp) REVERT: D 120 GLN cc_start: 0.6645 (pt0) cc_final: 0.6073 (pt0) REVERT: D 250 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6760 (t80) REVERT: d 10 LYS cc_start: 0.6670 (tttm) cc_final: 0.6000 (mttt) REVERT: d 67 ARG cc_start: 0.6205 (mmt-90) cc_final: 0.5101 (ptm-80) REVERT: E 17 PHE cc_start: 0.6747 (t80) cc_final: 0.6326 (t80) REVERT: E 40 ARG cc_start: 0.6014 (ttt180) cc_final: 0.5171 (mmt180) REVERT: e 12 ARG cc_start: 0.6351 (mpt180) cc_final: 0.5918 (mmp80) REVERT: e 27 ARG cc_start: 0.7837 (mtt90) cc_final: 0.6972 (ptp-110) REVERT: f 109 MET cc_start: 0.5010 (OUTLIER) cc_final: 0.4696 (tmm) REVERT: G 42 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7734 (mmtm) REVERT: G 185 SER cc_start: 0.8169 (t) cc_final: 0.7908 (p) REVERT: G 198 ARG cc_start: 0.6437 (ttp80) cc_final: 0.6140 (ttp80) REVERT: H 32 MET cc_start: 0.8214 (mpp) cc_final: 0.7766 (mpp) REVERT: H 217 MET cc_start: 0.6186 (tpp) cc_final: 0.5109 (ttt) REVERT: h 17 TRP cc_start: 0.4285 (OUTLIER) cc_final: 0.3562 (p-90) REVERT: h 183 LYS cc_start: 0.7064 (tmtt) cc_final: 0.6318 (mptt) REVERT: h 304 ASP cc_start: 0.7192 (t0) cc_final: 0.6555 (p0) REVERT: I 32 MET cc_start: 0.5237 (tpt) cc_final: 0.4789 (mtp) REVERT: I 37 LYS cc_start: 0.4592 (mmtm) cc_final: 0.3908 (pttt) REVERT: I 115 LYS cc_start: 0.6407 (tttp) cc_final: 0.5887 (ttmt) REVERT: I 173 PHE cc_start: 0.7267 (m-80) cc_final: 0.6950 (m-80) REVERT: J 77 ARG cc_start: 0.7060 (ttm110) cc_final: 0.6764 (ttm110) REVERT: J 79 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7706 (mp) REVERT: J 165 GLN cc_start: 0.6614 (pt0) cc_final: 0.5586 (mm-40) REVERT: n 21 ARG cc_start: 0.5268 (ttm170) cc_final: 0.4673 (ttp-110) REVERT: K 27 GLN cc_start: 0.7405 (tp40) cc_final: 0.7014 (tp40) REVERT: K 55 LYS cc_start: 0.6648 (ttmt) cc_final: 0.6185 (mttm) REVERT: K 66 LYS cc_start: 0.8201 (tttt) cc_final: 0.7738 (mmtm) REVERT: K 75 ASN cc_start: 0.6531 (t0) cc_final: 0.6082 (t0) REVERT: K 79 ARG cc_start: 0.7489 (tpp80) cc_final: 0.6999 (mmp80) REVERT: K 117 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7447 (mm) REVERT: K 155 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7697 (mmtp) REVERT: x 651 HIS cc_start: 0.7045 (OUTLIER) cc_final: 0.6802 (m-70) REVERT: x 796 PHE cc_start: 0.7645 (m-80) cc_final: 0.7361 (t80) REVERT: x 909 LYS cc_start: 0.4659 (pttp) cc_final: 0.3597 (mttt) REVERT: x 921 LYS cc_start: 0.7540 (tptp) cc_final: 0.6973 (tmmt) REVERT: x 1006 ILE cc_start: 0.6599 (pt) cc_final: 0.5947 (mm) REVERT: x 1029 TYR cc_start: 0.4587 (p90) cc_final: 0.4350 (p90) REVERT: x 1038 ARG cc_start: 0.6422 (ptt180) cc_final: 0.5760 (ptm-80) REVERT: x 1073 ASP cc_start: 0.6922 (m-30) cc_final: 0.6317 (t0) REVERT: x 1083 LYS cc_start: 0.6415 (tttt) cc_final: 0.6041 (pttm) REVERT: x 1206 GLN cc_start: 0.8409 (tp40) cc_final: 0.8149 (pt0) REVERT: L 27 VAL cc_start: 0.7613 (m) cc_final: 0.7368 (p) REVERT: M 5 GLN cc_start: 0.7130 (mp10) cc_final: 0.6836 (mp10) REVERT: M 7 GLU cc_start: 0.8011 (pm20) cc_final: 0.7503 (pm20) REVERT: M 67 SER cc_start: 0.8852 (t) cc_final: 0.8480 (m) REVERT: N 99 LYS cc_start: 0.3294 (pptt) cc_final: 0.3032 (pttm) REVERT: O 32 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7109 (t0) REVERT: O 100 LYS cc_start: 0.8275 (tppt) cc_final: 0.8042 (tttm) REVERT: P 37 PHE cc_start: 0.8326 (m-80) cc_final: 0.8097 (m-10) REVERT: P 87 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5526 (pt0) REVERT: P 135 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7404 (mt) REVERT: P 138 ASP cc_start: 0.5369 (OUTLIER) cc_final: 0.5003 (p0) REVERT: Q 30 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.5155 (t80) REVERT: R 41 MET cc_start: 0.7402 (tpp) cc_final: 0.7131 (tpp) REVERT: R 42 ILE cc_start: 0.7941 (mm) cc_final: 0.7465 (tp) REVERT: S 24 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7319 (mm) REVERT: T 83 PHE cc_start: 0.6575 (t80) cc_final: 0.6152 (t80) REVERT: T 134 GLN cc_start: 0.5988 (mm110) cc_final: 0.5403 (mm-40) REVERT: U 28 LEU cc_start: 0.7688 (mp) cc_final: 0.7459 (tp) REVERT: U 35 ASP cc_start: 0.6496 (OUTLIER) cc_final: 0.6126 (t0) REVERT: U 51 ASN cc_start: 0.8029 (m-40) cc_final: 0.7803 (m-40) REVERT: U 83 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5085 (mt0) REVERT: U 108 GLU cc_start: 0.7841 (pp20) cc_final: 0.7631 (pp20) REVERT: V 48 LEU cc_start: 0.3801 (OUTLIER) cc_final: 0.3112 (tt) REVERT: W 33 GLN cc_start: 0.8182 (tp40) cc_final: 0.7843 (tp40) REVERT: X 32 LYS cc_start: 0.8906 (tppt) cc_final: 0.8212 (ttpt) REVERT: X 78 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6641 (mmm-85) REVERT: X 88 LYS cc_start: 0.7612 (ttmm) cc_final: 0.7030 (tmtt) REVERT: Y 93 PHE cc_start: 0.7571 (m-10) cc_final: 0.7289 (m-10) REVERT: Y 105 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.5999 (m-80) REVERT: Y 127 ASN cc_start: 0.8324 (m110) cc_final: 0.7982 (t0) outliers start: 234 outliers final: 188 residues processed: 841 average time/residue: 0.8155 time to fit residues: 1179.5557 Evaluate side-chains 864 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 655 time to evaluate : 5.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain a residue 45 ASN Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 31 TYR Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 75 GLU Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 132 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 197 GLN Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 29 ASP Chi-restraints excluded: chain h residue 41 ILE Chi-restraints excluded: chain h residue 91 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 196 ASN Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 252 THR Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 153 LYS Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain x residue 633 CYS Chi-restraints excluded: chain x residue 651 HIS Chi-restraints excluded: chain x residue 652 THR Chi-restraints excluded: chain x residue 673 LEU Chi-restraints excluded: chain x residue 709 ASN Chi-restraints excluded: chain x residue 742 LEU Chi-restraints excluded: chain x residue 747 CYS Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 858 VAL Chi-restraints excluded: chain x residue 884 ASP Chi-restraints excluded: chain x residue 945 LEU Chi-restraints excluded: chain x residue 979 VAL Chi-restraints excluded: chain x residue 985 THR Chi-restraints excluded: chain x residue 999 SER Chi-restraints excluded: chain x residue 1014 LYS Chi-restraints excluded: chain x residue 1028 GLN Chi-restraints excluded: chain x residue 1031 VAL Chi-restraints excluded: chain x residue 1042 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 87 GLU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 83 GLN Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 78 ARG Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 440 optimal weight: 30.0000 chunk 709 optimal weight: 6.9990 chunk 433 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 chunk 493 optimal weight: 30.0000 chunk 744 optimal weight: 1.9990 chunk 684 optimal weight: 20.0000 chunk 592 optimal weight: 0.9990 chunk 61 optimal weight: 30.0000 chunk 457 optimal weight: 8.9990 chunk 363 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 45 ASN B 169 HIS D 113 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 159 ASN ** h 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN O 62 GLN P 26 ASN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 142 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN U 63 HIS ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 93743 Z= 0.168 Angle : 0.562 13.550 136219 Z= 0.284 Chirality : 0.035 0.273 16874 Planarity : 0.004 0.069 9815 Dihedral : 22.666 178.842 37727 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.16 % Favored : 93.82 % Rotamer: Outliers : 3.93 % Allowed : 23.93 % Favored : 72.13 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.16 (0.11), residues: 5551 helix: 0.68 (0.13), residues: 1693 sheet: -0.98 (0.17), residues: 909 loop : -1.61 (0.11), residues: 2949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP h 17 HIS 0.011 0.001 HIS h 64 PHE 0.025 0.001 PHE h 65 TYR 0.031 0.001 TYR B 156 ARG 0.012 0.000 ARG Z 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11102 Ramachandran restraints generated. 5551 Oldfield, 0 Emsley, 5551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 694 time to evaluate : 5.379 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: Z 113 ARG cc_start: 0.8406 (mmm160) cc_final: 0.7986 (mtm-85) REVERT: A 46 ARG cc_start: 0.5152 (mtm180) cc_final: 0.4477 (ptp-170) REVERT: A 111 GLU cc_start: 0.5418 (OUTLIER) cc_final: 0.5059 (pm20) REVERT: A 114 LYS cc_start: 0.3507 (mmtm) cc_final: 0.3172 (mttt) REVERT: a 52 LYS cc_start: 0.7459 (tptp) cc_final: 0.6718 (pttp) REVERT: a 78 LYS cc_start: 0.6692 (mttp) cc_final: 0.6213 (mmtm) REVERT: a 108 ILE cc_start: 0.8652 (pt) cc_final: 0.8278 (mt) REVERT: a 112 ASN cc_start: 0.6132 (t0) cc_final: 0.5141 (p0) REVERT: B 80 ARG cc_start: 0.7013 (mmm-85) cc_final: 0.6808 (mmm160) REVERT: B 104 THR cc_start: 0.6831 (t) cc_final: 0.6605 (t) REVERT: B 128 ARG cc_start: 0.7497 (tpp-160) cc_final: 0.6836 (mmm160) REVERT: B 132 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6940 (mt0) REVERT: B 156 TYR cc_start: 0.8245 (m-80) cc_final: 0.8043 (m-80) REVERT: B 205 ARG cc_start: 0.5129 (OUTLIER) cc_final: 0.4869 (ptm160) REVERT: b 33 ASP cc_start: 0.8423 (p0) cc_final: 0.7587 (p0) REVERT: C 224 GLU cc_start: 0.5867 (pp20) cc_final: 0.5005 (tp30) REVERT: c 15 GLU cc_start: 0.7242 (tp30) cc_final: 0.6722 (tp30) REVERT: D 72 ASP cc_start: 0.5745 (t70) cc_final: 0.5174 (t70) REVERT: D 105 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: D 120 GLN cc_start: 0.6740 (pt0) cc_final: 0.6086 (pt0) REVERT: D 249 SER cc_start: 0.9042 (m) cc_final: 0.8677 (p) REVERT: D 250 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6576 (t80) REVERT: d 10 LYS cc_start: 0.6722 (tttm) cc_final: 0.6013 (mttt) REVERT: d 67 ARG cc_start: 0.6185 (mmt-90) cc_final: 0.5033 (ptm-80) REVERT: E 17 PHE cc_start: 0.6669 (t80) cc_final: 0.6457 (t80) REVERT: E 40 ARG cc_start: 0.6051 (ttt180) cc_final: 0.5187 (mmt180) REVERT: E 127 MET cc_start: 0.7716 (mmm) cc_final: 0.7487 (mmm) REVERT: e 27 ARG cc_start: 0.7775 (mtt90) cc_final: 0.6949 (ptp-110) REVERT: G 42 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7673 (mmtm) REVERT: G 185 SER cc_start: 0.8106 (t) cc_final: 0.7864 (p) REVERT: G 198 ARG cc_start: 0.6401 (ttp80) cc_final: 0.6123 (ttp80) REVERT: H 32 MET cc_start: 0.8151 (mpp) cc_final: 0.7799 (mpp) REVERT: H 84 TYR cc_start: 0.7001 (t80) cc_final: 0.6769 (t80) REVERT: H 217 MET cc_start: 0.6189 (tpp) cc_final: 0.5099 (ttt) REVERT: h 183 LYS cc_start: 0.7111 (tmtt) cc_final: 0.6398 (mptt) REVERT: h 304 ASP cc_start: 0.7065 (t0) cc_final: 0.6386 (p0) REVERT: I 32 MET cc_start: 0.5378 (tpt) cc_final: 0.4928 (mtp) REVERT: I 37 LYS cc_start: 0.4514 (mmtm) cc_final: 0.3824 (pttt) REVERT: I 115 LYS cc_start: 0.6338 (tttp) cc_final: 0.5814 (ttmt) REVERT: I 173 PHE cc_start: 0.7319 (m-80) cc_final: 0.7027 (m-80) REVERT: J 77 ARG cc_start: 0.7057 (ttm110) cc_final: 0.6781 (ttm110) REVERT: J 79 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7747 (mp) REVERT: J 165 GLN cc_start: 0.6618 (pt0) cc_final: 0.5642 (mm-40) REVERT: n 21 ARG cc_start: 0.5231 (ttm170) cc_final: 0.4640 (ttp-110) REVERT: K 55 LYS cc_start: 0.6607 (ttmt) cc_final: 0.6137 (mttm) REVERT: K 66 LYS cc_start: 0.8205 (tttt) cc_final: 0.7722 (mmtm) REVERT: K 75 ASN cc_start: 0.6478 (t0) cc_final: 0.6058 (t0) REVERT: K 79 ARG cc_start: 0.7495 (tpp80) cc_final: 0.7027 (mmp80) REVERT: K 117 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7575 (mm) REVERT: K 155 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7732 (mmtp) REVERT: x 651 HIS cc_start: 0.7098 (OUTLIER) cc_final: 0.6883 (m-70) REVERT: x 796 PHE cc_start: 0.7626 (m-80) cc_final: 0.7347 (t80) REVERT: x 909 LYS cc_start: 0.4675 (pttp) cc_final: 0.3614 (mttt) REVERT: x 1006 ILE cc_start: 0.6526 (pt) cc_final: 0.5890 (mm) REVERT: x 1038 ARG cc_start: 0.6485 (ptt180) cc_final: 0.5840 (ptm-80) REVERT: x 1073 ASP cc_start: 0.6892 (m-30) cc_final: 0.6269 (t0) REVERT: x 1083 LYS cc_start: 0.6348 (tttt) cc_final: 0.5970 (pttm) REVERT: x 1206 GLN cc_start: 0.8446 (tp40) cc_final: 0.8186 (pt0) REVERT: L 27 VAL cc_start: 0.7630 (m) cc_final: 0.7383 (p) REVERT: M 5 GLN cc_start: 0.7140 (mp10) cc_final: 0.6771 (mp10) REVERT: M 7 GLU cc_start: 0.7950 (pm20) cc_final: 0.7444 (pm20) REVERT: M 67 SER cc_start: 0.8777 (t) cc_final: 0.8401 (m) REVERT: N 99 LYS cc_start: 0.3309 (pptt) cc_final: 0.3021 (pttm) REVERT: O 32 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.6978 (t0) REVERT: O 100 LYS cc_start: 0.8277 (tppt) cc_final: 0.8063 (tttm) REVERT: P 37 PHE cc_start: 0.8369 (m-80) cc_final: 0.8161 (m-10) REVERT: P 87 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5515 (pt0) REVERT: P 135 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7351 (mt) REVERT: P 138 ASP cc_start: 0.5427 (OUTLIER) cc_final: 0.5060 (p0) REVERT: Q 30 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.4910 (t80) REVERT: R 41 MET cc_start: 0.7332 (tpp) cc_final: 0.7074 (tpp) REVERT: R 42 ILE cc_start: 0.7844 (mm) cc_final: 0.7280 (tp) REVERT: R 114 GLN cc_start: 0.7633 (pp30) cc_final: 0.7389 (pp30) REVERT: S 24 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7464 (mm) REVERT: T 83 PHE cc_start: 0.6436 (t80) cc_final: 0.6006 (t80) REVERT: T 134 GLN cc_start: 0.6020 (mm110) cc_final: 0.5475 (mm-40) REVERT: U 28 LEU cc_start: 0.7710 (mp) cc_final: 0.7396 (tp) REVERT: U 35 ASP cc_start: 0.6449 (OUTLIER) cc_final: 0.6076 (t0) REVERT: U 44 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6756 (tp30) REVERT: U 51 ASN cc_start: 0.8034 (m-40) cc_final: 0.7832 (m-40) REVERT: U 83 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5160 (tt0) REVERT: W 33 GLN cc_start: 0.8184 (tp40) cc_final: 0.7862 (tp40) REVERT: X 32 LYS cc_start: 0.8910 (tppt) cc_final: 0.8234 (ttpt) REVERT: X 78 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6920 (mmt-90) REVERT: X 88 LYS cc_start: 0.7623 (ttmm) cc_final: 0.7068 (tmtt) REVERT: Y 93 PHE cc_start: 0.7509 (m-10) cc_final: 0.7195 (m-10) REVERT: Y 105 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.5879 (m-80) REVERT: Y 127 ASN cc_start: 0.8373 (m110) cc_final: 0.8026 (t0) outliers start: 191 outliers final: 157 residues processed: 825 average time/residue: 0.8154 time to fit residues: 1159.9620 Evaluate side-chains 834 residues out of total 4861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 659 time to evaluate : 5.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain a residue 45 ASN Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 31 TYR Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain f residue 132 SER Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 197 GLN Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 29 ASP Chi-restraints excluded: chain h residue 41 ILE Chi-restraints excluded: chain h residue 91 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 196 ASN Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 252 THR Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 153 LYS Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain x residue 633 CYS Chi-restraints excluded: chain x residue 651 HIS Chi-restraints excluded: chain x residue 673 LEU Chi-restraints excluded: chain x residue 709 ASN Chi-restraints excluded: chain x residue 742 LEU Chi-restraints excluded: chain x residue 747 CYS Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 858 VAL Chi-restraints excluded: chain x residue 945 LEU Chi-restraints excluded: chain x residue 979 VAL Chi-restraints excluded: chain x residue 999 SER Chi-restraints excluded: chain x residue 1014 LYS Chi-restraints excluded: chain x residue 1028 GLN Chi-restraints excluded: chain x residue 1031 VAL Chi-restraints excluded: chain x residue 1042 ASP Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 87 GLU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 83 GLN Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 103 VAL Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 78 ARG Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 747 random chunks: chunk 470 optimal weight: 0.5980 chunk 631 optimal weight: 8.9990 chunk 181 optimal weight: 0.5980 chunk 546 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 593 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 609 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN O 62 GLN P 26 ASN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN U 63 HIS ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.115172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094025 restraints weight = 228551.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.094357 restraints weight = 312377.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095024 restraints weight = 211574.664| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.207 93743 Z= 0.227 Angle : 0.637 59.175 136219 Z= 0.338 Chirality : 0.038 1.706 16874 Planarity : 0.005 0.182 9815 Dihedral : 22.665 178.843 37727 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.03 % Favored : 93.95 % Rotamer: Outliers : 3.93 % Allowed : 24.04 % Favored : 72.03 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.16 (0.11), residues: 5551 helix: 0.69 (0.13), residues: 1693 sheet: -0.98 (0.17), residues: 908 loop : -1.60 (0.11), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP h 17 HIS 0.010 0.001 HIS h 64 PHE 0.022 0.001 PHE x 785 TYR 0.028 0.001 TYR B 156 ARG 0.010 0.000 ARG Z 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19493.53 seconds wall clock time: 344 minutes 46.23 seconds (20686.23 seconds total)