Starting phenix.real_space_refine on Fri Mar 22 07:36:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/03_2024/6khi_9989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/03_2024/6khi_9989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/03_2024/6khi_9989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/03_2024/6khi_9989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/03_2024/6khi_9989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/03_2024/6khi_9989_updated.pdb" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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= 0.007 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: 6 Type Number sf(0) Gaussians Fe 14 7.16 5 P 6 5.49 5 S 184 5.16 5 C 21526 2.51 5 N 5162 2.21 5 O 5743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 388": "NH1" <-> "NH2" Residue "F ARG 459": "NH1" <-> "NH2" Residue "F GLU 464": "OE1" <-> "OE2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 512": "OE1" <-> "OE2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "F ARG 634": "NH1" <-> "NH2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G ARG 166": "NH1" <-> "NH2" Residue "G ARG 167": "NH1" <-> "NH2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H ARG 226": "NH1" <-> "NH2" Residue "H GLU 241": "OE1" <-> "OE2" Residue "H ARG 277": "NH1" <-> "NH2" Residue "H ARG 330": "NH1" <-> "NH2" Residue "H ARG 352": "NH1" <-> "NH2" Residue "I ARG 33": "NH1" <-> "NH2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I GLU 133": "OE1" <-> "OE2" Residue "I ARG 179": "NH1" <-> "NH2" Residue "J ARG 90": "NH1" <-> "NH2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 151": "NH1" <-> "NH2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "L GLU 6": "OE1" <-> "OE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M GLU 55": "OE1" <-> "OE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M ARG 72": "NH1" <-> "NH2" Residue "M ARG 82": "NH1" <-> "NH2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N ARG 36": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N GLU 112": "OE1" <-> "OE2" Residue "N ARG 136": "NH1" <-> "NH2" Residue "O ARG 44": "NH1" <-> "NH2" Residue "V GLU 50": "OE1" <-> "OE2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V GLU 72": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "V GLU 115": "OE1" <-> "OE2" Residue "1 GLU 31": "OE1" <-> "OE2" Residue "1 GLU 72": "OE1" <-> "OE2" Residue "1 ARG 84": "NH1" <-> "NH2" Residue "1 GLU 94": "OE1" <-> "OE2" Residue "1 GLU 95": "OE1" <-> "OE2" Residue "1 GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32635 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2821 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Chain: "B" Number of atoms: 3724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3724 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 18, 'TRANS': 473} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 971 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3897 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 26, 'TRANS': 477} Chain: "E" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 775 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain: "F" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 4945 Classifications: {'peptide': 641} Link IDs: {'PTRANS': 32, 'TRANS': 608} Chain breaks: 2 Chain: "G" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1278 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3177 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain: "I" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1537 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain: "J" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1307 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 11, 'TRANS': 148} Chain: "K" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1590 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 20, 'TRANS': 184} Chain: "L" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "N" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 11, 'TRANS': 136} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "P" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 321 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 333 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "S" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 469 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "V" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "1" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 756 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 124 Unusual residues: {'DGD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'LHG': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "D" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'BCR': 2, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'LHG': 3, 'LMG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 41 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'LHG': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22426 SG CYS I 103 51.247 147.432 125.066 1.00 26.51 S ATOM 22470 SG CYS I 109 46.922 151.988 124.714 1.00 32.39 S ATOM 22175 SG CYS I 73 46.055 146.638 121.137 1.00 29.12 S ATOM 22451 SG CYS I 106 50.504 150.648 119.533 1.00 28.97 S ATOM 22122 SG CYS I 66 36.063 154.706 125.280 1.00 42.91 S ATOM 22144 SG CYS I 69 40.935 150.705 125.903 1.00 35.01 S ATOM 22103 SG CYS I 63 38.256 153.294 131.116 1.00 46.30 S ATOM 22504 SG CYS I 113 41.754 156.985 127.101 1.00 38.42 S ATOM 25530 SG CYS K 148 57.799 145.760 118.845 1.00 30.02 S ATOM 24806 SG CYS K 53 62.990 142.480 120.310 1.00 30.13 S ATOM 24800 SG CYS K 52 61.997 143.616 114.451 1.00 33.10 S ATOM 25304 SG CYS K 117 57.766 139.725 117.520 1.00 26.14 S ATOM 31484 SG CYS 1 41 32.927 160.609 122.910 1.00 83.69 S ATOM 31515 SG CYS 1 46 30.656 158.601 125.006 1.00 81.81 S ATOM 31534 SG CYS 1 49 27.912 161.206 121.565 1.00 94.03 S ATOM 31764 SG CYS 1 79 29.354 164.549 121.962 1.00100.16 S Time building chain proxies: 16.28, per 1000 atoms: 0.50 Number of scatterers: 32635 At special positions: 0 Unit cell: (168.48, 203.84, 172.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 14 26.01 S 184 16.00 P 6 15.00 O 5743 8.00 N 5162 7.00 C 21526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.82 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 1 101 " pdb="FE2 FES 1 101 " - pdb=" SG CYS 1 49 " pdb="FE1 FES 1 101 " - pdb=" SG CYS 1 41 " pdb="FE1 FES 1 101 " - pdb=" SG CYS 1 46 " pdb="FE2 FES 1 101 " - pdb=" SG CYS 1 79 " pdb=" SF4 I 202 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 103 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 73 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 106 " pdb=" SF4 I 203 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 63 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 69 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 113 " pdb=" SF4 K 301 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 52 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 117 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 53 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 148 " Number of angles added : 42 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 161 helices and 14 sheets defined 52.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.46 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 22 through 59 Proline residue: A 31 - end of helix removed outlier: 4.228A pdb=" N MET A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 85 Proline residue: A 76 - end of helix removed outlier: 4.125A pdb=" N LYS A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 84 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 Proline residue: A 103 - end of helix Proline residue: A 109 - end of helix removed outlier: 4.401A pdb=" N TYR A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 151 removed outlier: 3.836A pdb=" N ILE A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 4.554A pdb=" N LEU A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.668A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 213 through 226 removed outlier: 3.811A pdb=" N LEU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 275 removed outlier: 3.891A pdb=" N TYR A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 300 through 329 Processing helix chain 'A' and resid 341 through 344 No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 348 through 365 Processing helix chain 'B' and resid 15 through 34 removed outlier: 3.847A pdb=" N THR B 19 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 20 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 24 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE B 34 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.889A pdb=" N ARG B 41 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 62 removed outlier: 3.711A pdb=" N ILE B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 78 through 97 Processing helix chain 'B' and resid 101 through 104 No H-bonds generated for 'chain 'B' and resid 101 through 104' Processing helix chain 'B' and resid 110 through 127 removed outlier: 3.870A pdb=" N ILE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 150 Processing helix chain 'B' and resid 157 through 187 removed outlier: 3.675A pdb=" N ILE B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 208 through 223 removed outlier: 3.666A pdb=" N PHE B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 238 removed outlier: 5.374A pdb=" N GLN B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TRP B 231 " --> pdb=" O PHE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.182A pdb=" N TYR B 236 " --> pdb=" O PRO B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 263 removed outlier: 4.232A pdb=" N SER B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 290 Processing helix chain 'B' and resid 299 through 320 removed outlier: 3.588A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 353 removed outlier: 3.833A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 370 through 384 Processing helix chain 'B' and resid 390 through 403 removed outlier: 4.396A pdb=" N GLY B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 433 removed outlier: 3.905A pdb=" N TYR B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 445 No H-bonds generated for 'chain 'B' and resid 442 through 445' Processing helix chain 'B' and resid 457 through 476 removed outlier: 4.298A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLY B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 486 Processing helix chain 'C' and resid 19 through 42 removed outlier: 3.735A pdb=" N GLY C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Proline residue: C 33 - end of helix Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 74 through 98 removed outlier: 3.970A pdb=" N ALA C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Proline residue: C 93 - end of helix removed outlier: 3.615A pdb=" N PHE C 98 " --> pdb=" O TRP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 125 Processing helix chain 'D' and resid 6 through 18 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 32 through 56 removed outlier: 3.848A pdb=" N TRP D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 108 removed outlier: 4.021A pdb=" N TRP D 107 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Proline residue: D 108 - end of helix Processing helix chain 'D' and resid 113 through 132 removed outlier: 4.403A pdb=" N GLY D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 removed outlier: 4.312A pdb=" N GLU D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 162 through 188 removed outlier: 3.785A pdb=" N GLY D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 176 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.933A pdb=" N LYS D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 238 No H-bonds generated for 'chain 'D' and resid 235 through 238' Processing helix chain 'D' and resid 244 through 250 removed outlier: 3.832A pdb=" N LEU D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 264 No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 271 through 296 removed outlier: 3.851A pdb=" N LYS D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 303 through 322 removed outlier: 4.169A pdb=" N ILE D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 357 removed outlier: 4.166A pdb=" N GLY D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 371 No H-bonds generated for 'chain 'D' and resid 368 through 371' Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 393 through 406 removed outlier: 3.826A pdb=" N ALA D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 441 removed outlier: 4.066A pdb=" N GLY D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) Proline residue: D 431 - end of helix removed outlier: 4.076A pdb=" N LEU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 479 Proline residue: D 473 - end of helix Processing helix chain 'D' and resid 481 through 483 No H-bonds generated for 'chain 'D' and resid 481 through 483' Processing helix chain 'D' and resid 485 through 498 removed outlier: 5.421A pdb=" N ALA D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR D 491 " --> pdb=" O ILE D 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'E' and resid 27 through 51 removed outlier: 3.665A pdb=" N LEU E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 87 removed outlier: 3.668A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'F' and resid 3 through 6 No H-bonds generated for 'chain 'F' and resid 3 through 6' Processing helix chain 'F' and resid 8 through 27 removed outlier: 3.680A pdb=" N ILE F 11 " --> pdb=" O ALA F 8 " (cutoff:3.500A) Proline residue: F 12 - end of helix Proline residue: F 15 - end of helix removed outlier: 4.050A pdb=" N ILE F 21 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL F 22 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY F 23 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE F 27 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 33 No H-bonds generated for 'chain 'F' and resid 30 through 33' Processing helix chain 'F' and resid 37 through 63 removed outlier: 4.288A pdb=" N GLY F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 117 removed outlier: 3.969A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N HIS F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 139 removed outlier: 3.782A pdb=" N LEU F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 162 removed outlier: 4.304A pdb=" N TRP F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 199 removed outlier: 3.811A pdb=" N GLY F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLY F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU F 191 " --> pdb=" O PHE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 removed outlier: 4.118A pdb=" N ASP F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 240 removed outlier: 4.120A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.740A pdb=" N MET F 254 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU F 255 " --> pdb=" O PRO F 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 250 through 255' Processing helix chain 'F' and resid 258 through 266 removed outlier: 3.892A pdb=" N HIS F 265 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 279 removed outlier: 4.263A pdb=" N GLY F 273 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL F 274 " --> pdb=" O ALA F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 284 No H-bonds generated for 'chain 'F' and resid 281 through 284' Processing helix chain 'F' and resid 288 through 308 Processing helix chain 'F' and resid 317 through 335 Processing helix chain 'F' and resid 339 through 348 Processing helix chain 'F' and resid 353 through 368 removed outlier: 3.885A pdb=" N LEU F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 383 No H-bonds generated for 'chain 'F' and resid 381 through 383' Processing helix chain 'F' and resid 387 through 390 No H-bonds generated for 'chain 'F' and resid 387 through 390' Processing helix chain 'F' and resid 392 through 402 removed outlier: 4.981A pdb=" N GLY F 401 " --> pdb=" O THR F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 427 removed outlier: 3.776A pdb=" N GLU F 419 " --> pdb=" O TRP F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 454 removed outlier: 4.208A pdb=" N LEU F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU F 437 " --> pdb=" O LEU F 433 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY F 440 " --> pdb=" O TRP F 436 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 492 Proline residue: F 489 - end of helix Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 500 through 504 Processing helix chain 'F' and resid 510 through 514 Processing helix chain 'F' and resid 532 through 555 removed outlier: 3.971A pdb=" N SER F 539 " --> pdb=" O ILE F 535 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY F 544 " --> pdb=" O SER F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 568 Processing helix chain 'F' and resid 570 through 577 Processing helix chain 'F' and resid 579 through 588 removed outlier: 3.548A pdb=" N PHE F 582 " --> pdb=" O LYS F 579 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP F 583 " --> pdb=" O TRP F 580 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU F 584 " --> pdb=" O TYR F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 619 removed outlier: 4.473A pdb=" N VAL F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP F 610 " --> pdb=" O TYR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 630 No H-bonds generated for 'chain 'F' and resid 628 through 630' Processing helix chain 'F' and resid 635 through 654 removed outlier: 3.823A pdb=" N SER F 653 " --> pdb=" O PHE F 649 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 654 " --> pdb=" O VAL F 650 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 27 removed outlier: 3.945A pdb=" N THR G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 52 removed outlier: 3.979A pdb=" N GLY G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 70 through 76 Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 131 through 140 removed outlier: 3.913A pdb=" N PHE G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 164 removed outlier: 3.970A pdb=" N SER G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 57 removed outlier: 3.704A pdb=" N GLU H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 76 through 90 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 96 through 125 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 130 through 148 removed outlier: 4.223A pdb=" N PHE H 135 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ARG H 138 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU H 139 " --> pdb=" O ARG H 136 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR H 140 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA H 147 " --> pdb=" O LEU H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 191 removed outlier: 4.652A pdb=" N VAL H 173 " --> pdb=" O TYR H 170 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR H 174 " --> pdb=" O GLY H 171 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS H 175 " --> pdb=" O TRP H 172 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU H 184 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 3.836A pdb=" N GLU H 191 " --> pdb=" O ASP H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 204 Processing helix chain 'H' and resid 212 through 218 Processing helix chain 'H' and resid 222 through 224 No H-bonds generated for 'chain 'H' and resid 222 through 224' Processing helix chain 'H' and resid 258 through 282 removed outlier: 3.551A pdb=" N VAL H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 297 Processing helix chain 'H' and resid 377 through 385 Processing helix chain 'I' and resid 4 through 29 Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 108 through 111 No H-bonds generated for 'chain 'I' and resid 108 through 111' Processing helix chain 'I' and resid 132 through 134 No H-bonds generated for 'chain 'I' and resid 132 through 134' Processing helix chain 'I' and resid 184 through 192 Processing helix chain 'J' and resid 46 through 54 Processing helix chain 'J' and resid 119 through 128 Processing helix chain 'J' and resid 162 through 164 No H-bonds generated for 'chain 'J' and resid 162 through 164' Processing helix chain 'K' and resid 26 through 40 Processing helix chain 'K' and resid 52 through 61 removed outlier: 3.818A pdb=" N ALA K 59 " --> pdb=" O GLU K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 70 No H-bonds generated for 'chain 'K' and resid 68 through 70' Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'K' and resid 94 through 103 Processing helix chain 'K' and resid 116 through 119 No H-bonds generated for 'chain 'K' and resid 116 through 119' Processing helix chain 'K' and resid 122 through 124 No H-bonds generated for 'chain 'K' and resid 122 through 124' Processing helix chain 'K' and resid 135 through 137 No H-bonds generated for 'chain 'K' and resid 135 through 137' Processing helix chain 'K' and resid 152 through 166 Processing helix chain 'L' and resid 6 through 21 Processing helix chain 'L' and resid 23 through 34 Processing helix chain 'L' and resid 41 through 53 Processing helix chain 'L' and resid 55 through 64 Proline residue: L 63 - end of helix Processing helix chain 'M' and resid 45 through 59 Processing helix chain 'M' and resid 67 through 87 Processing helix chain 'N' and resid 8 through 16 Processing helix chain 'N' and resid 31 through 40 removed outlier: 3.593A pdb=" N LYS N 40 " --> pdb=" O ARG N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 55 through 58 No H-bonds generated for 'chain 'N' and resid 55 through 58' Processing helix chain 'N' and resid 83 through 89 removed outlier: 3.714A pdb=" N LEU N 88 " --> pdb=" O VAL N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 122 removed outlier: 3.634A pdb=" N LEU N 116 " --> pdb=" O GLU N 112 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 146 No H-bonds generated for 'chain 'N' and resid 143 through 146' Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'P' and resid 7 through 26 Proline residue: P 16 - end of helix Processing helix chain 'Q' and resid 18 through 41 Processing helix chain 'V' and resid 45 through 50 Processing helix chain 'V' and resid 52 through 58 Processing helix chain 'V' and resid 126 through 139 Processing helix chain '1' and resid 26 through 33 Processing helix chain '1' and resid 68 through 71 No H-bonds generated for 'chain '1' and resid 68 through 71' Processing helix chain '1' and resid 78 through 80 No H-bonds generated for 'chain '1' and resid 78 through 80' Processing helix chain '1' and resid 95 through 97 No H-bonds generated for 'chain '1' and resid 95 through 97' Processing sheet with id= A, first strand: chain 'F' and resid 69 through 76 removed outlier: 6.809A pdb=" N ILE F 83 " --> pdb=" O TRP F 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 27 through 30 Processing sheet with id= C, first strand: chain 'H' and resid 327 through 331 Processing sheet with id= D, first strand: chain 'I' and resid 56 through 58 Processing sheet with id= E, first strand: chain 'J' and resid 37 through 41 Processing sheet with id= F, first strand: chain 'J' and resid 60 through 62 Processing sheet with id= G, first strand: chain 'K' and resid 83 through 86 removed outlier: 6.684A pdb=" N TYR K 110 " --> pdb=" O ILE K 84 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR K 86 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE K 112 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL K 143 " --> pdb=" O ALA K 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'M' and resid 15 through 17 Processing sheet with id= I, first strand: chain 'N' and resid 19 through 22 Processing sheet with id= J, first strand: chain 'N' and resid 43 through 47 Processing sheet with id= K, first strand: chain 'O' and resid 9 through 11 Processing sheet with id= L, first strand: chain 'O' and resid 59 through 62 removed outlier: 6.098A pdb=" N LYS O 51 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL O 40 " --> pdb=" O LYS O 51 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 95 through 97 removed outlier: 6.673A pdb=" N ALA S 76 " --> pdb=" O GLN S 68 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE S 70 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '1' and resid 16 through 20 removed outlier: 3.805A pdb=" N THR 1 16 " --> pdb=" O LEU 1 8 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS 1 87 " --> pdb=" O THR 1 7 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL 1 9 " --> pdb=" O CYS 1 87 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE 1 89 " --> pdb=" O VAL 1 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU 1 55 " --> pdb=" O LYS 1 88 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU 1 90 " --> pdb=" O LEU 1 53 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU 1 53 " --> pdb=" O LEU 1 90 " (cutoff:3.500A) 1413 hydrogen bonds defined for protein. 4002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.24 Time building geometry restraints manager: 12.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 13448 1.40 - 1.63: 19646 1.63 - 1.85: 315 1.85 - 2.07: 0 2.07 - 2.29: 40 Bond restraints: 33449 Sorted by residual: bond pdb=" C6 SQD L 101 " pdb=" S SQD L 101 " ideal model delta sigma weight residual 1.840 1.616 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C6 SQD D 601 " pdb=" S SQD D 601 " ideal model delta sigma weight residual 1.840 1.618 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C6 SQD C 201 " pdb=" S SQD C 201 " ideal model delta sigma weight residual 1.840 1.621 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C25 BCR D 602 " pdb=" C26 BCR D 602 " ideal model delta sigma weight residual 1.347 1.557 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C25 BCR D 603 " pdb=" C26 BCR D 603 " ideal model delta sigma weight residual 1.347 1.554 -0.207 2.00e-02 2.50e+03 1.08e+02 ... (remaining 33444 not shown) Histogram of bond angle deviations from ideal: 72.07 - 86.10: 42 86.10 - 100.14: 30 100.14 - 114.17: 20405 114.17 - 128.21: 24653 128.21 - 142.25: 330 Bond angle restraints: 45460 Sorted by residual: angle pdb=" C6 SQD C 201 " pdb=" S SQD C 201 " pdb=" O7 SQD C 201 " ideal model delta sigma weight residual 111.32 73.52 37.80 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C6 SQD D 601 " pdb=" S SQD D 601 " pdb=" O7 SQD D 601 " ideal model delta sigma weight residual 111.32 73.66 37.66 3.00e+00 1.11e-01 1.58e+02 angle pdb=" S1 FES 1 101 " pdb="FE2 FES 1 101 " pdb=" S2 FES 1 101 " ideal model delta sigma weight residual 104.33 90.06 14.27 1.14e+00 7.69e-01 1.57e+02 angle pdb=" C6 SQD L 101 " pdb=" S SQD L 101 " pdb=" O7 SQD L 101 " ideal model delta sigma weight residual 111.32 73.99 37.33 3.00e+00 1.11e-01 1.55e+02 angle pdb=" S1 FES 1 101 " pdb="FE1 FES 1 101 " pdb=" S2 FES 1 101 " ideal model delta sigma weight residual 104.33 90.10 14.23 1.20e+00 6.94e-01 1.41e+02 ... (remaining 45455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 18334 24.77 - 49.53: 1202 49.53 - 74.30: 184 74.30 - 99.06: 33 99.06 - 123.83: 34 Dihedral angle restraints: 19787 sinusoidal: 8004 harmonic: 11783 Sorted by residual: dihedral pdb=" CA TYR H 72 " pdb=" C TYR H 72 " pdb=" N ALA H 73 " pdb=" CA ALA H 73 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP H 71 " pdb=" C ASP H 71 " pdb=" N TYR H 72 " pdb=" CA TYR H 72 " ideal model delta harmonic sigma weight residual -180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA PRO I 164 " pdb=" C PRO I 164 " pdb=" N ALA I 165 " pdb=" CA ALA I 165 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 19784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.933: 5208 0.933 - 1.867: 0 1.867 - 2.800: 0 2.800 - 3.734: 0 3.734 - 4.667: 1 Chirality restraints: 5209 Sorted by residual: chirality pdb=" C1 SQD D 601 " pdb=" C2 SQD D 601 " pdb=" O5 SQD D 601 " pdb=" O6 SQD D 601 " both_signs ideal model delta sigma weight residual False -2.39 2.28 -4.67 2.00e-01 2.50e+01 5.45e+02 chirality pdb="FE1 SF4 K 301 " pdb=" S2 SF4 K 301 " pdb=" S3 SF4 K 301 " pdb=" S4 SF4 K 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" CB ILE H 154 " pdb=" CA ILE H 154 " pdb=" CG1 ILE H 154 " pdb=" CG2 ILE H 154 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 5206 not shown) Planarity restraints: 5614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 BCR D 603 " -0.279 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C17 BCR D 603 " 0.558 2.00e-02 2.50e+03 pdb=" C18 BCR D 603 " -0.290 2.00e-02 2.50e+03 pdb=" C19 BCR D 603 " -0.028 2.00e-02 2.50e+03 pdb=" C36 BCR D 603 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR D 602 " 0.491 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C11 BCR D 602 " -0.243 2.00e-02 2.50e+03 pdb=" C34 BCR D 602 " 0.110 2.00e-02 2.50e+03 pdb=" C8 BCR D 602 " -0.047 2.00e-02 2.50e+03 pdb=" C9 BCR D 602 " -0.311 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 BCR D 602 " -0.135 2.00e-02 2.50e+03 2.61e-01 8.52e+02 pdb=" C13 BCR D 602 " 0.327 2.00e-02 2.50e+03 pdb=" C14 BCR D 602 " -0.419 2.00e-02 2.50e+03 pdb=" C15 BCR D 602 " 0.199 2.00e-02 2.50e+03 pdb=" C35 BCR D 602 " 0.028 2.00e-02 2.50e+03 ... (remaining 5611 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8008 2.79 - 3.31: 30089 3.31 - 3.84: 58724 3.84 - 4.37: 70745 4.37 - 4.90: 119169 Nonbonded interactions: 286735 Sorted by model distance: nonbonded pdb=" OH TYR C 75 " pdb=" O ALA E 75 " model vdw 2.257 2.440 nonbonded pdb=" O ALA B 39 " pdb=" OG1 THR B 43 " model vdw 2.276 2.440 nonbonded pdb=" O ALA D 322 " pdb=" OH TYR D 411 " model vdw 2.287 2.440 nonbonded pdb=" OD1 ASP H 359 " pdb=" OG SER H 391 " model vdw 2.287 2.440 nonbonded pdb=" OE1 GLN B 310 " pdb=" OH TYR B 332 " model vdw 2.290 2.440 ... (remaining 286730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 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: 0.030 Extract box with map and model: 15.550 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 90.380 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.224 33449 Z= 0.547 Angle : 1.251 37.802 45460 Z= 0.573 Chirality : 0.087 4.667 5209 Planarity : 0.012 0.309 5614 Dihedral : 17.454 123.826 12251 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.94 % Favored : 91.03 % Rotamer: Outliers : 0.27 % Allowed : 7.74 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.35 (0.10), residues: 4049 helix: -2.51 (0.08), residues: 2285 sheet: -2.96 (0.34), residues: 168 loop : -3.28 (0.13), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 274 HIS 0.010 0.001 HIS D 339 PHE 0.033 0.002 PHE A 321 TYR 0.034 0.002 TYR A 245 ARG 0.015 0.001 ARG H 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 592 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 291 MET cc_start: 0.8769 (mmm) cc_final: 0.8343 (mmt) REVERT: G 95 LEU cc_start: 0.8151 (mt) cc_final: 0.7759 (pp) REVERT: H 22 MET cc_start: 0.6152 (mtp) cc_final: 0.5933 (tmt) REVERT: H 71 ASP cc_start: 0.5282 (p0) cc_final: 0.5081 (p0) REVERT: K 144 TYR cc_start: 0.8717 (m-80) cc_final: 0.8502 (m-80) REVERT: N 106 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7884 (mtmt) REVERT: 1 93 GLN cc_start: 0.7363 (mm110) cc_final: 0.6929 (mm-40) REVERT: 1 96 GLU cc_start: 0.7827 (mp0) cc_final: 0.7268 (mp0) outliers start: 9 outliers final: 4 residues processed: 600 average time/residue: 1.3888 time to fit residues: 989.8555 Evaluate side-chains 395 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 391 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain Q residue 9 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 4.9990 chunk 304 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 315 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 234 optimal weight: 0.5980 chunk 365 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN A 339 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS B 296 GLN B 340 ASN B 404 GLN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS E 2 GLN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 HIS F 349 HIS F 570 GLN G 62 GLN G 71 ASN H 48 HIS H 205 GLN I 6 GLN K 80 GLN K 181 HIS L 70 GLN M 9 HIS M 37 ASN N 90 ASN S 64 GLN V 49 ASN V 86 GLN 1 70 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33449 Z= 0.177 Angle : 0.648 9.246 45460 Z= 0.315 Chirality : 0.042 0.171 5209 Planarity : 0.005 0.072 5614 Dihedral : 12.864 107.437 5050 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.61 % Favored : 92.37 % Rotamer: Outliers : 2.64 % Allowed : 15.60 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.61 (0.12), residues: 4049 helix: -0.86 (0.10), residues: 2287 sheet: -2.65 (0.35), residues: 177 loop : -2.89 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 274 HIS 0.004 0.001 HIS M 9 PHE 0.025 0.001 PHE B 228 TYR 0.022 0.001 TYR A 245 ARG 0.008 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 442 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6762 (p0) REVERT: D 268 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6708 (m-30) REVERT: D 413 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7525 (tm) REVERT: F 193 MET cc_start: 0.7369 (ptm) cc_final: 0.7123 (ptm) REVERT: G 95 LEU cc_start: 0.8230 (mt) cc_final: 0.7852 (OUTLIER) REVERT: H 22 MET cc_start: 0.6061 (mtp) cc_final: 0.5818 (tmt) REVERT: J 67 TYR cc_start: 0.8558 (p90) cc_final: 0.8132 (p90) REVERT: K 27 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7690 (tp) REVERT: K 144 TYR cc_start: 0.8711 (m-80) cc_final: 0.8505 (m-80) REVERT: L 47 MET cc_start: 0.7641 (mmt) cc_final: 0.7286 (mtp) REVERT: 1 4 TYR cc_start: 0.7074 (m-80) cc_final: 0.6855 (m-10) outliers start: 89 outliers final: 32 residues processed: 489 average time/residue: 1.2551 time to fit residues: 744.3127 Evaluate side-chains 428 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 393 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain 1 residue 18 ILE Chi-restraints excluded: chain 1 residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 303 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 365 optimal weight: 0.0470 chunk 395 optimal weight: 7.9990 chunk 325 optimal weight: 0.6980 chunk 362 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS H 239 HIS I 57 HIS K 80 GLN P 36 GLN S 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33449 Z= 0.266 Angle : 0.649 9.034 45460 Z= 0.320 Chirality : 0.043 0.171 5209 Planarity : 0.005 0.070 5614 Dihedral : 10.866 109.119 5048 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.65 % Allowed : 17.38 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.79 (0.13), residues: 4049 helix: -0.16 (0.11), residues: 2296 sheet: -2.60 (0.35), residues: 183 loop : -2.55 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 107 HIS 0.006 0.001 HIS H 327 PHE 0.023 0.001 PHE L 49 TYR 0.022 0.002 TYR A 245 ARG 0.008 0.000 ARG H 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 407 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 LEU cc_start: 0.8189 (mt) cc_final: 0.7776 (pp) REVERT: H 22 MET cc_start: 0.6172 (mtp) cc_final: 0.5918 (tmt) REVERT: J 100 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8425 (m) REVERT: K 27 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7720 (tp) REVERT: L 47 MET cc_start: 0.7590 (mmt) cc_final: 0.7300 (mtp) REVERT: M 77 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9064 (tt) REVERT: P 21 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8407 (mp) REVERT: V 49 ASN cc_start: 0.7173 (m110) cc_final: 0.6912 (m110) REVERT: 1 4 TYR cc_start: 0.7190 (m-80) cc_final: 0.6930 (m-10) outliers start: 123 outliers final: 56 residues processed: 482 average time/residue: 1.2282 time to fit residues: 721.4813 Evaluate side-chains 445 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 385 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 106 LYS Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 18 ILE Chi-restraints excluded: chain 1 residue 37 LEU Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 4.9990 chunk 274 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 174 optimal weight: 6.9990 chunk 245 optimal weight: 0.6980 chunk 367 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 191 optimal weight: 0.8980 chunk 347 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 208 ASN A 212 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 447 ASN F 182 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN K 80 GLN S 64 GLN V 135 GLN 1 93 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33449 Z= 0.191 Angle : 0.605 9.549 45460 Z= 0.299 Chirality : 0.042 0.177 5209 Planarity : 0.004 0.067 5614 Dihedral : 10.057 107.446 5045 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.62 % Allowed : 19.19 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.35 (0.13), residues: 4049 helix: 0.23 (0.11), residues: 2295 sheet: -2.66 (0.35), residues: 184 loop : -2.37 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 107 HIS 0.004 0.001 HIS D 339 PHE 0.019 0.001 PHE A 321 TYR 0.025 0.001 TYR L 31 ARG 0.009 0.000 ARG H 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 422 time to evaluate : 3.777 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6745 (p0) REVERT: B 339 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8182 (ptt) REVERT: D 250 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8885 (mp) REVERT: D 321 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.7969 (tp) REVERT: D 413 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7551 (tm) REVERT: D 437 MET cc_start: 0.7983 (ppp) cc_final: 0.7779 (ptm) REVERT: E 100 LYS cc_start: 0.8489 (mtmm) cc_final: 0.8043 (mtpt) REVERT: F 193 MET cc_start: 0.7413 (ptm) cc_final: 0.7108 (ptm) REVERT: G 95 LEU cc_start: 0.8191 (mt) cc_final: 0.7796 (pp) REVERT: H 22 MET cc_start: 0.6204 (mtp) cc_final: 0.5956 (tmt) REVERT: J 100 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8405 (m) REVERT: L 47 MET cc_start: 0.7614 (mmt) cc_final: 0.7335 (mtp) REVERT: N 89 GLU cc_start: 0.7134 (mp0) cc_final: 0.6814 (mp0) REVERT: V 49 ASN cc_start: 0.7274 (m110) cc_final: 0.6996 (m110) REVERT: 1 1 MET cc_start: 0.4378 (OUTLIER) cc_final: 0.3432 (tmm) outliers start: 122 outliers final: 60 residues processed: 497 average time/residue: 1.2335 time to fit residues: 747.7907 Evaluate side-chains 451 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 384 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 368 GLN Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 106 LYS Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 18 ILE Chi-restraints excluded: chain 1 residue 37 LEU Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 289 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 331 optimal weight: 0.0170 chunk 268 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 198 optimal weight: 0.9980 chunk 348 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 563 GLN K 80 GLN K 170 HIS S 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33449 Z= 0.213 Angle : 0.621 18.308 45460 Z= 0.304 Chirality : 0.042 0.188 5209 Planarity : 0.004 0.066 5614 Dihedral : 9.803 108.386 5045 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.74 % Allowed : 19.93 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.13), residues: 4049 helix: 0.44 (0.11), residues: 2287 sheet: -2.64 (0.34), residues: 201 loop : -2.23 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 107 HIS 0.007 0.001 HIS D 247 PHE 0.025 0.001 PHE F 131 TYR 0.022 0.001 TYR K 48 ARG 0.010 0.000 ARG H 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 396 time to evaluate : 3.864 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6759 (p0) REVERT: B 339 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8189 (ptt) REVERT: D 250 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8937 (mp) REVERT: D 321 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7922 (tp) REVERT: D 413 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7585 (tm) REVERT: E 100 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8216 (mtpt) REVERT: F 208 MET cc_start: 0.8197 (mtp) cc_final: 0.7962 (mtt) REVERT: G 95 LEU cc_start: 0.8207 (mt) cc_final: 0.7808 (pp) REVERT: H 22 MET cc_start: 0.6196 (mtp) cc_final: 0.5914 (tmt) REVERT: H 224 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7901 (ttt) REVERT: I 87 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: J 100 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8438 (m) REVERT: K 27 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7763 (tp) REVERT: V 49 ASN cc_start: 0.7372 (m110) cc_final: 0.7131 (m110) REVERT: V 121 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7711 (pp20) REVERT: V 128 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8530 (tp) outliers start: 126 outliers final: 66 residues processed: 480 average time/residue: 1.2344 time to fit residues: 725.6468 Evaluate side-chains 452 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 375 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 368 GLN Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 106 LYS Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 18 ILE Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 388 optimal weight: 0.8980 chunk 322 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN S 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33449 Z= 0.200 Angle : 0.616 12.501 45460 Z= 0.303 Chirality : 0.042 0.234 5209 Planarity : 0.004 0.065 5614 Dihedral : 9.583 108.051 5045 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 3.74 % Allowed : 20.56 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.14), residues: 4049 helix: 0.59 (0.11), residues: 2288 sheet: -2.31 (0.36), residues: 185 loop : -2.20 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 107 HIS 0.005 0.001 HIS D 247 PHE 0.028 0.001 PHE F 131 TYR 0.024 0.001 TYR K 48 ARG 0.008 0.000 ARG H 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 396 time to evaluate : 3.403 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6756 (p0) REVERT: B 339 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8140 (ptt) REVERT: D 250 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8971 (mp) REVERT: D 321 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7906 (tp) REVERT: D 413 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7520 (tm) REVERT: F 193 MET cc_start: 0.7399 (ptm) cc_final: 0.7087 (ptm) REVERT: G 95 LEU cc_start: 0.8119 (mt) cc_final: 0.7747 (pp) REVERT: H 22 MET cc_start: 0.6191 (mtp) cc_final: 0.5912 (tmt) REVERT: I 87 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: J 100 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8480 (m) REVERT: K 27 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7775 (tp) REVERT: L 66 ASN cc_start: 0.8138 (t0) cc_final: 0.7928 (t0) REVERT: V 49 ASN cc_start: 0.7396 (m110) cc_final: 0.7183 (m110) REVERT: V 84 MET cc_start: 0.6901 (mmm) cc_final: 0.6330 (tpp) REVERT: V 118 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8569 (pp) REVERT: V 128 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8559 (tp) outliers start: 126 outliers final: 64 residues processed: 480 average time/residue: 1.2429 time to fit residues: 727.6939 Evaluate side-chains 446 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 372 time to evaluate : 4.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 106 LYS Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain V residue 118 LEU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 4.9990 chunk 43 optimal weight: 0.0000 chunk 221 optimal weight: 1.9990 chunk 284 optimal weight: 5.9990 chunk 220 optimal weight: 0.1980 chunk 327 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 chunk 387 optimal weight: 6.9990 chunk 242 optimal weight: 0.2980 chunk 236 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 122 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN K 80 GLN N 87 HIS S 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33449 Z= 0.166 Angle : 0.603 12.809 45460 Z= 0.296 Chirality : 0.041 0.211 5209 Planarity : 0.004 0.065 5614 Dihedral : 9.297 107.236 5045 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.38 % Allowed : 21.51 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.14), residues: 4049 helix: 0.75 (0.11), residues: 2275 sheet: -2.37 (0.34), residues: 195 loop : -2.11 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 274 HIS 0.004 0.001 HIS D 339 PHE 0.034 0.001 PHE F 131 TYR 0.030 0.001 TYR I 20 ARG 0.006 0.000 ARG H 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 409 time to evaluate : 3.924 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6801 (p0) REVERT: B 339 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8115 (ptt) REVERT: D 321 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7754 (tp) REVERT: D 413 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7500 (tm) REVERT: F 193 MET cc_start: 0.7312 (ptm) cc_final: 0.7013 (ptm) REVERT: F 208 MET cc_start: 0.7964 (mtt) cc_final: 0.7395 (mtp) REVERT: G 95 LEU cc_start: 0.8108 (mt) cc_final: 0.7744 (OUTLIER) REVERT: H 22 MET cc_start: 0.6168 (mtp) cc_final: 0.5902 (tmt) REVERT: J 100 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8435 (m) REVERT: K 27 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7714 (tp) REVERT: L 66 ASN cc_start: 0.8103 (t0) cc_final: 0.7873 (t0) REVERT: P 21 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8371 (mp) REVERT: V 49 ASN cc_start: 0.7547 (m110) cc_final: 0.7318 (m110) REVERT: V 84 MET cc_start: 0.6883 (mmm) cc_final: 0.6503 (tmm) REVERT: V 128 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8557 (tp) outliers start: 114 outliers final: 64 residues processed: 482 average time/residue: 1.1870 time to fit residues: 702.7521 Evaluate side-chains 449 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 378 time to evaluate : 3.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 80 GLN Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 40 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 246 optimal weight: 0.5980 chunk 263 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 304 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN S 64 GLN V 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33449 Z= 0.189 Angle : 0.611 13.025 45460 Z= 0.300 Chirality : 0.042 0.214 5209 Planarity : 0.004 0.064 5614 Dihedral : 9.203 107.612 5045 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.17 % Allowed : 21.89 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.14), residues: 4049 helix: 0.83 (0.11), residues: 2271 sheet: -2.34 (0.34), residues: 196 loop : -2.05 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 274 HIS 0.008 0.001 HIS D 239 PHE 0.028 0.001 PHE F 131 TYR 0.023 0.001 TYR K 48 ARG 0.006 0.000 ARG V 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 379 time to evaluate : 3.702 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6801 (p0) REVERT: B 339 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8142 (ptt) REVERT: D 321 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7811 (tp) REVERT: D 413 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7505 (tm) REVERT: F 45 MET cc_start: 0.8574 (mmt) cc_final: 0.8364 (mtp) REVERT: F 193 MET cc_start: 0.7363 (ptm) cc_final: 0.7062 (ptm) REVERT: F 208 MET cc_start: 0.7961 (mtt) cc_final: 0.7460 (mtp) REVERT: G 95 LEU cc_start: 0.8118 (mt) cc_final: 0.7756 (OUTLIER) REVERT: H 22 MET cc_start: 0.6179 (mtp) cc_final: 0.5891 (tmt) REVERT: H 389 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7856 (mpp) REVERT: J 100 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8461 (m) REVERT: K 27 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7754 (tp) REVERT: L 66 ASN cc_start: 0.8087 (t0) cc_final: 0.7868 (t0) REVERT: P 21 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8358 (mp) REVERT: V 49 ASN cc_start: 0.7595 (m110) cc_final: 0.7366 (m110) REVERT: V 84 MET cc_start: 0.6871 (mmm) cc_final: 0.6521 (tmm) outliers start: 107 outliers final: 71 residues processed: 446 average time/residue: 1.2271 time to fit residues: 673.3658 Evaluate side-chains 441 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 363 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 0.6980 chunk 371 optimal weight: 0.9990 chunk 338 optimal weight: 4.9990 chunk 361 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 283 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 326 optimal weight: 3.9990 chunk 341 optimal weight: 0.9990 chunk 359 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN V 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33449 Z= 0.197 Angle : 0.624 13.798 45460 Z= 0.305 Chirality : 0.042 0.234 5209 Planarity : 0.004 0.065 5614 Dihedral : 9.128 107.808 5045 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.00 % Allowed : 22.25 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.14), residues: 4049 helix: 0.86 (0.11), residues: 2276 sheet: -2.28 (0.34), residues: 196 loop : -2.01 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 107 HIS 0.008 0.001 HIS D 239 PHE 0.025 0.001 PHE 1 39 TYR 0.024 0.001 TYR I 20 ARG 0.005 0.000 ARG H 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 376 time to evaluate : 3.831 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6768 (p0) REVERT: B 339 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8178 (ptt) REVERT: D 321 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7846 (tp) REVERT: D 448 LYS cc_start: 0.7088 (mmpt) cc_final: 0.6862 (mmtm) REVERT: E 100 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8194 (mtpt) REVERT: F 193 MET cc_start: 0.7375 (ptm) cc_final: 0.7068 (ptm) REVERT: F 208 MET cc_start: 0.7977 (mtt) cc_final: 0.7459 (mtp) REVERT: G 95 LEU cc_start: 0.8146 (mt) cc_final: 0.7748 (pp) REVERT: H 22 MET cc_start: 0.6217 (mtp) cc_final: 0.5909 (tmt) REVERT: J 100 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8473 (m) REVERT: K 27 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7750 (tp) REVERT: L 66 ASN cc_start: 0.8092 (t0) cc_final: 0.7875 (t0) REVERT: P 21 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8374 (mp) REVERT: V 49 ASN cc_start: 0.7679 (m110) cc_final: 0.7440 (m110) REVERT: V 84 MET cc_start: 0.6857 (mmm) cc_final: 0.6512 (tmm) REVERT: 1 1 MET cc_start: 0.5393 (OUTLIER) cc_final: 0.5156 (ptp) outliers start: 101 outliers final: 71 residues processed: 439 average time/residue: 1.1969 time to fit residues: 643.9058 Evaluate side-chains 456 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 378 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 0.7980 chunk 381 optimal weight: 0.9980 chunk 233 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 400 optimal weight: 2.9990 chunk 368 optimal weight: 0.0170 chunk 318 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 246 optimal weight: 0.5980 chunk 195 optimal weight: 4.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN V 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33449 Z= 0.182 Angle : 0.624 13.247 45460 Z= 0.304 Chirality : 0.042 0.263 5209 Planarity : 0.004 0.065 5614 Dihedral : 9.041 107.729 5045 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.43 % Allowed : 22.90 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.14), residues: 4049 helix: 0.93 (0.11), residues: 2266 sheet: -2.27 (0.34), residues: 196 loop : -1.97 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 274 HIS 0.008 0.001 HIS D 239 PHE 0.024 0.001 PHE 1 39 TYR 0.032 0.001 TYR H 182 ARG 0.005 0.000 ARG V 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 390 time to evaluate : 3.674 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6759 (p0) REVERT: B 339 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8184 (ptt) REVERT: D 321 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7764 (tp) REVERT: D 448 LYS cc_start: 0.7075 (mmpt) cc_final: 0.6854 (mmtm) REVERT: E 100 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8127 (mtpt) REVERT: F 193 MET cc_start: 0.7356 (ptm) cc_final: 0.7060 (ptm) REVERT: G 95 LEU cc_start: 0.8153 (mt) cc_final: 0.7755 (pp) REVERT: J 100 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8464 (m) REVERT: K 27 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7759 (tp) REVERT: L 66 ASN cc_start: 0.8050 (t0) cc_final: 0.7827 (t0) REVERT: P 21 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8365 (mp) REVERT: V 84 MET cc_start: 0.6827 (mmm) cc_final: 0.6495 (tmm) REVERT: 1 8 LEU cc_start: 0.8994 (mm) cc_final: 0.8759 (mp) REVERT: 1 69 ASP cc_start: 0.7669 (m-30) cc_final: 0.7373 (m-30) REVERT: 1 80 VAL cc_start: 0.8834 (m) cc_final: 0.8278 (m) outliers start: 82 outliers final: 66 residues processed: 441 average time/residue: 1.2072 time to fit residues: 652.6668 Evaluate side-chains 448 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 376 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 115 GLU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 3.9990 chunk 339 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 319 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 327 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN V 49 ASN V 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.096445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.080869 restraints weight = 70489.840| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.88 r_work: 0.3251 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 33449 Z= 0.299 Angle : 0.677 13.352 45460 Z= 0.332 Chirality : 0.044 0.274 5209 Planarity : 0.004 0.064 5614 Dihedral : 9.236 106.927 5045 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.79 % Allowed : 22.66 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.14), residues: 4049 helix: 0.82 (0.11), residues: 2279 sheet: -2.27 (0.34), residues: 198 loop : -1.99 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 107 HIS 0.010 0.001 HIS D 239 PHE 0.024 0.001 PHE A 321 TYR 0.030 0.002 TYR H 182 ARG 0.005 0.000 ARG V 122 =============================================================================== Job complete usr+sys time: 11869.80 seconds wall clock time: 210 minutes 50.91 seconds (12650.91 seconds total)