Starting phenix.real_space_refine on Sat Feb 17 05:56:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mur_9253/02_2024/6mur_9253_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mur_9253/02_2024/6mur_9253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mur_9253/02_2024/6mur_9253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mur_9253/02_2024/6mur_9253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mur_9253/02_2024/6mur_9253_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mur_9253/02_2024/6mur_9253_neut.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Zn 3 6.06 5 P 45 5.49 5 S 49 5.16 5 C 11077 2.51 5 N 3100 2.21 5 O 3386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ARG 755": "NH1" <-> "NH2" Residue "A ARG 777": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 4": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 383": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17660 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6150 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1143 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2214 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 1 Chain: "D" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2284 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2261 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 20, 'TRANS': 265} Chain: "G" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 589 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 13} Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 398 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 13} Chain: "F" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2618 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 10, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 250 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3074 SG CYS A 389 52.089 81.889 90.850 1.00 45.72 S ATOM 3094 SG CYS A 392 49.588 78.659 91.791 1.00 45.83 S ATOM 3249 SG CYS A 413 51.023 81.803 93.938 1.00 59.14 S ATOM 3269 SG CYS A 416 52.416 78.520 93.867 1.00 56.75 S ATOM 8120 SG CYS C 113 61.837 95.927 64.287 1.00 35.30 S ATOM 8187 SG CYS C 122 62.149 94.984 60.481 1.00 30.50 S ATOM 8207 SG CYS C 125 59.882 92.574 63.344 1.00 28.05 S ATOM 10404 SG CYS D 113 86.902 72.810 63.408 1.00 41.86 S ATOM 10471 SG CYS D 122 88.371 73.176 59.968 1.00 38.85 S ATOM 10491 SG CYS D 125 84.383 71.335 60.917 1.00 31.93 S Time building chain proxies: 9.65, per 1000 atoms: 0.55 Number of scatterers: 17660 At special positions: 0 Unit cell: (120.879, 113.256, 156.816, 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) Zn 3 29.99 S 49 16.00 P 45 15.00 O 3386 8.00 N 3100 7.00 C 11077 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: 7.08 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 111 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " Number of angles added : 12 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 31 sheets defined 40.0% alpha, 14.6% beta 12 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 6.04 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.576A pdb=" N ALA A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 29 through 44 removed outlier: 3.774A pdb=" N GLN A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.890A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.799A pdb=" N ARG A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.661A pdb=" N ARG A 82 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 106 removed outlier: 3.947A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.511A pdb=" N TYR A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.698A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 removed outlier: 3.581A pdb=" N ALA A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.908A pdb=" N TYR A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 303 through 325 removed outlier: 4.268A pdb=" N GLU A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.607A pdb=" N LYS A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.670A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.711A pdb=" N PHE A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 549 removed outlier: 3.682A pdb=" N ARG A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.646A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.523A pdb=" N GLU A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 649 removed outlier: 3.516A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 647 " --> pdb=" O ARG A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 688 removed outlier: 3.730A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.842A pdb=" N LEU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 4.316A pdb=" N TYR A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'A' and resid 764 through 775 removed outlier: 4.456A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.634A pdb=" N LYS B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 63 removed outlier: 4.083A pdb=" N ALA B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 53 " --> pdb=" O TRP B 49 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 72 through 88 removed outlier: 3.826A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 88 " --> pdb=" O TYR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 110 removed outlier: 3.931A pdb=" N VAL B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 removed outlier: 3.834A pdb=" N VAL B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 156 removed outlier: 4.170A pdb=" N PHE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.556A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 70 removed outlier: 3.621A pdb=" N LEU C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.697A pdb=" N ARG C 75 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 122 through 129 removed outlier: 3.746A pdb=" N LEU C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.697A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP C 156 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.775A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 3.626A pdb=" N PHE C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'D' and resid 51 through 70 removed outlier: 3.573A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.563A pdb=" N GLU D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP D 156 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 247 through 254 removed outlier: 3.923A pdb=" N TYR D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.741A pdb=" N ILE D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'E' and resid 21 through 36 removed outlier: 4.202A pdb=" N ALA E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE E 35 " --> pdb=" O ALA E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 51 removed outlier: 3.550A pdb=" N VAL E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 99 removed outlier: 3.522A pdb=" N TYR E 90 " --> pdb=" O GLU E 86 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 99 " --> pdb=" O ARG E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 removed outlier: 4.035A pdb=" N GLU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 Processing helix chain 'E' and resid 171 through 179 removed outlier: 3.855A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 51 through 60 removed outlier: 4.014A pdb=" N LEU F 58 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 71 Processing helix chain 'F' and resid 113 through 133 removed outlier: 3.547A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 123 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.702A pdb=" N ARG F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 142' Processing helix chain 'F' and resid 148 through 156 removed outlier: 3.690A pdb=" N ARG F 156 " --> pdb=" O ARG F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 removed outlier: 4.483A pdb=" N SER F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 168 " --> pdb=" O TYR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 187 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 257 through 262 removed outlier: 3.559A pdb=" N LEU F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.538A pdb=" N LYS F 276 " --> pdb=" O TRP F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 304 removed outlier: 3.952A pdb=" N TRP F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR F 298 " --> pdb=" O ASP F 294 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA F 299 " --> pdb=" O GLU F 295 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 304 " --> pdb=" O VAL F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 326 removed outlier: 3.749A pdb=" N SER F 324 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU F 326 " --> pdb=" O TYR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 removed outlier: 3.951A pdb=" N LEU F 348 " --> pdb=" O THR F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 removed outlier: 3.559A pdb=" N ASN F 359 " --> pdb=" O TYR F 355 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.724A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 345 through 346 removed outlier: 3.602A pdb=" N GLU A 346 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 349 " --> pdb=" O GLU A 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 386 through 389 removed outlier: 3.805A pdb=" N ARG A 394 " --> pdb=" O CYS A 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 402 through 403 removed outlier: 3.777A pdb=" N VAL A 412 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.985A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 450 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 580 through 585 removed outlier: 6.650A pdb=" N PHE A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AA8, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.727A pdb=" N ARG A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.800A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.800A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 242 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS C 14 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE C 240 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS C 16 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N PHE C 238 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.551A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLY C 87 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB4, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB5, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.960A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.960A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY D 13 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP D 241 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE D 243 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 85 through 88 removed outlier: 7.272A pdb=" N SER D 85 " --> pdb=" O PHE D 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB9, first strand: chain 'D' and resid 163 through 171 removed outlier: 3.514A pdb=" N ARG D 181 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 170 " --> pdb=" O ASN D 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 58 through 61 removed outlier: 3.518A pdb=" N TYR E 60 " --> pdb=" O GLY E 156 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 157 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 58 through 61 removed outlier: 3.518A pdb=" N TYR E 60 " --> pdb=" O GLY E 156 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 157 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'E' and resid 124 through 125 Processing sheet with id=AC5, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.807A pdb=" N TYR E 144 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 252 through 253 removed outlier: 4.578A pdb=" N TYR E 211 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 282 " --> pdb=" O TYR E 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 229 through 232 removed outlier: 3.605A pdb=" N LYS E 232 " --> pdb=" O MET E 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC9, first strand: chain 'E' and resid 261 through 263 Processing sheet with id=AD1, first strand: chain 'F' and resid 250 through 251 removed outlier: 3.652A pdb=" N VAL F 251 " --> pdb=" O ARG F 4 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 15 through 20 removed outlier: 5.602A pdb=" N ASN F 18 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 100 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 209 through 211 Processing sheet with id=AD4, first strand: chain 'F' and resid 236 through 243 removed outlier: 3.631A pdb=" N ILE F 236 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU F 385 " --> pdb=" O GLU F 228 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4684 1.33 - 1.45: 3638 1.45 - 1.57: 9636 1.57 - 1.69: 89 1.69 - 1.81: 80 Bond restraints: 18127 Sorted by residual: bond pdb=" N LEU E 219 " pdb=" CA LEU E 219 " ideal model delta sigma weight residual 1.458 1.501 -0.043 7.40e-03 1.83e+04 3.40e+01 bond pdb=" C GLU A 388 " pdb=" O GLU A 388 " ideal model delta sigma weight residual 1.236 1.290 -0.054 1.21e-02 6.83e+03 2.01e+01 bond pdb=" N GLY F 365 " pdb=" CA GLY F 365 " ideal model delta sigma weight residual 1.447 1.486 -0.039 1.09e-02 8.42e+03 1.29e+01 bond pdb=" C LEU A 396 " pdb=" N PRO A 397 " ideal model delta sigma weight residual 1.332 1.288 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" N ILE A 16 " pdb=" CA ILE A 16 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.61e+00 ... (remaining 18122 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.27: 727 106.27 - 113.48: 9703 113.48 - 120.69: 8162 120.69 - 127.90: 5898 127.90 - 135.11: 236 Bond angle restraints: 24726 Sorted by residual: angle pdb=" C ASN D 179 " pdb=" N PRO D 180 " pdb=" CA PRO D 180 " ideal model delta sigma weight residual 119.76 128.44 -8.68 1.03e+00 9.43e-01 7.09e+01 angle pdb=" N PRO F 61 " pdb=" CA PRO F 61 " pdb=" CB PRO F 61 " ideal model delta sigma weight residual 103.08 110.18 -7.10 9.70e-01 1.06e+00 5.36e+01 angle pdb=" N PRO F 79 " pdb=" CA PRO F 79 " pdb=" CB PRO F 79 " ideal model delta sigma weight residual 103.25 110.82 -7.57 1.05e+00 9.07e-01 5.19e+01 angle pdb=" N PRO F 62 " pdb=" CA PRO F 62 " pdb=" CB PRO F 62 " ideal model delta sigma weight residual 103.00 110.46 -7.46 1.10e+00 8.26e-01 4.60e+01 angle pdb=" N PRO F 191 " pdb=" CA PRO F 191 " pdb=" CB PRO F 191 " ideal model delta sigma weight residual 103.25 110.13 -6.88 1.05e+00 9.07e-01 4.30e+01 ... (remaining 24721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 10653 35.18 - 70.36: 216 70.36 - 105.54: 23 105.54 - 140.73: 0 140.73 - 175.91: 2 Dihedral angle restraints: 10894 sinusoidal: 4735 harmonic: 6159 Sorted by residual: dihedral pdb=" O4' C G 20 " pdb=" C1' C G 20 " pdb=" N1 C G 20 " pdb=" C2 C G 20 " ideal model delta sinusoidal sigma weight residual -128.00 47.91 -175.91 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C G 14 " pdb=" C1' C G 14 " pdb=" N1 C G 14 " pdb=" C2 C G 14 " ideal model delta sinusoidal sigma weight residual -128.00 37.13 -165.13 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" C ASP D 28 " pdb=" N ASP D 28 " pdb=" CA ASP D 28 " pdb=" CB ASP D 28 " ideal model delta harmonic sigma weight residual -122.60 -136.69 14.09 0 2.50e+00 1.60e-01 3.18e+01 ... (remaining 10891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2352 0.090 - 0.181: 338 0.181 - 0.271: 35 0.271 - 0.361: 3 0.361 - 0.452: 1 Chirality restraints: 2729 Sorted by residual: chirality pdb=" CA ASP D 28 " pdb=" N ASP D 28 " pdb=" C ASP D 28 " pdb=" CB ASP D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C1' C G 14 " pdb=" O4' C G 14 " pdb=" C2' C G 14 " pdb=" N1 C G 14 " both_signs ideal model delta sigma weight residual False 2.45 2.11 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA CYS A 389 " pdb=" N CYS A 389 " pdb=" C CYS A 389 " pdb=" CB CYS A 389 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2726 not shown) Planarity restraints: 3031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 392 " -0.024 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C CYS A 392 " 0.091 2.00e-02 2.50e+03 pdb=" O CYS A 392 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY A 393 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 47 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ALA E 47 " 0.057 2.00e-02 2.50e+03 pdb=" O ALA E 47 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE E 48 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C G 10 " 0.044 2.00e-02 2.50e+03 2.20e-02 1.08e+01 pdb=" N1 C G 10 " -0.045 2.00e-02 2.50e+03 pdb=" C2 C G 10 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C G 10 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C G 10 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C G 10 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C G 10 " 0.015 2.00e-02 2.50e+03 pdb=" C5 C G 10 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C G 10 " -0.007 2.00e-02 2.50e+03 ... (remaining 3028 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 149 2.57 - 3.15: 13357 3.15 - 3.74: 26803 3.74 - 4.32: 39114 4.32 - 4.90: 64444 Nonbonded interactions: 143867 Sorted by model distance: nonbonded pdb=" N2 G G 13 " pdb=" O2 C H 31 " model vdw 1.989 2.520 nonbonded pdb=" O ARG A 385 " pdb=" N GLU A 398 " model vdw 2.027 2.520 nonbonded pdb=" OH TYR B 125 " pdb=" CG2 THR F 37 " model vdw 2.078 3.460 nonbonded pdb=" O ALA D 130 " pdb=" O PHE D 137 " model vdw 2.120 3.040 nonbonded pdb=" N GLU F 38 " pdb=" OE1 GLU F 38 " model vdw 2.233 2.520 ... (remaining 143862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 4 through 27 or resid 34 through 287 or resid 301)) } 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: 1.040 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: 0.010 Extract box with map and model: 4.490 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 55.500 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 0.101 18127 Z= 0.553 Angle : 1.050 10.393 24726 Z= 0.616 Chirality : 0.064 0.452 2729 Planarity : 0.008 0.069 3031 Dihedral : 13.727 175.907 6958 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.43 % Favored : 92.43 % Rotamer: Outliers : 0.66 % Allowed : 5.09 % Favored : 94.25 % Cbeta Deviations : 0.05 % 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: -4.96 (0.14), residues: 2127 helix: -4.27 (0.09), residues: 807 sheet: -2.62 (0.28), residues: 282 loop : -2.55 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 320 HIS 0.013 0.002 HIS D 22 PHE 0.032 0.003 PHE D 194 TYR 0.029 0.003 TYR C 233 ARG 0.014 0.001 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 497 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7233 (tt0) cc_final: 0.7027 (tt0) REVERT: A 98 TYR cc_start: 0.6699 (t80) cc_final: 0.6204 (t80) REVERT: A 195 ILE cc_start: 0.8770 (pp) cc_final: 0.8456 (pt) REVERT: A 735 ARG cc_start: 0.7728 (ppp80) cc_final: 0.7509 (ptm160) REVERT: C 90 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.6817 (ttp-110) REVERT: D 115 ASP cc_start: 0.6446 (t70) cc_final: 0.6071 (t70) REVERT: D 177 GLN cc_start: 0.8142 (tp40) cc_final: 0.7902 (tp-100) REVERT: D 184 GLU cc_start: 0.7636 (tt0) cc_final: 0.7415 (tt0) REVERT: D 255 LYS cc_start: 0.6865 (mmtm) cc_final: 0.6656 (mmtt) REVERT: E 104 LEU cc_start: 0.8737 (tm) cc_final: 0.8466 (tp) REVERT: F 19 GLU cc_start: 0.7970 (mp0) cc_final: 0.7521 (mp0) REVERT: F 329 SER cc_start: 0.7083 (t) cc_final: 0.6804 (p) outliers start: 11 outliers final: 4 residues processed: 507 average time/residue: 0.3913 time to fit residues: 273.9301 Evaluate side-chains 278 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 274 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain D residue 183 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 196 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 HIS A 692 ASN B 77 ASN B 88 GLN C 136 ASN C 177 GLN C 179 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 179 ASN D 183 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 ASN F 107 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18127 Z= 0.183 Angle : 0.630 10.211 24726 Z= 0.327 Chirality : 0.044 0.189 2729 Planarity : 0.005 0.050 3031 Dihedral : 14.951 172.698 3109 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.81 % Allowed : 9.82 % Favored : 87.37 % 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: -3.52 (0.15), residues: 2127 helix: -2.48 (0.14), residues: 824 sheet: -1.88 (0.28), residues: 304 loop : -2.25 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 320 HIS 0.006 0.001 HIS A 61 PHE 0.026 0.002 PHE A 502 TYR 0.040 0.002 TYR B 125 ARG 0.006 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 327 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.7256 (ttm110) REVERT: A 98 TYR cc_start: 0.6769 (t80) cc_final: 0.6249 (t80) REVERT: A 167 LYS cc_start: 0.8378 (mttt) cc_final: 0.8059 (mttp) REVERT: A 195 ILE cc_start: 0.8777 (pp) cc_final: 0.8495 (pt) REVERT: A 245 ASP cc_start: 0.7628 (p0) cc_final: 0.7273 (p0) REVERT: A 438 ASN cc_start: 0.7398 (p0) cc_final: 0.7186 (p0) REVERT: A 629 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5740 (pt0) REVERT: A 705 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 735 ARG cc_start: 0.7859 (ppp80) cc_final: 0.7571 (ptm160) REVERT: A 777 ARG cc_start: 0.5700 (OUTLIER) cc_final: 0.5154 (ttt180) REVERT: C 90 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.6719 (ttp-110) REVERT: C 284 GLU cc_start: 0.5754 (mt-10) cc_final: 0.5503 (mt-10) REVERT: D 107 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7451 (mtm-85) REVERT: F 19 GLU cc_start: 0.7864 (mp0) cc_final: 0.7423 (mp0) REVERT: F 29 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5528 (mp0) REVERT: F 256 ASP cc_start: 0.7614 (t70) cc_final: 0.7380 (t70) REVERT: F 329 SER cc_start: 0.7085 (t) cc_final: 0.6740 (p) outliers start: 47 outliers final: 27 residues processed: 358 average time/residue: 0.3674 time to fit residues: 187.9434 Evaluate side-chains 292 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 261 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 196 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18127 Z= 0.310 Angle : 0.645 11.085 24726 Z= 0.330 Chirality : 0.046 0.173 2729 Planarity : 0.005 0.055 3031 Dihedral : 14.751 174.762 3104 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.77 % Allowed : 11.92 % Favored : 84.31 % 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: -2.67 (0.17), residues: 2127 helix: -1.38 (0.16), residues: 833 sheet: -1.63 (0.28), residues: 312 loop : -2.09 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 341 HIS 0.006 0.001 HIS A 61 PHE 0.029 0.002 PHE F 288 TYR 0.021 0.002 TYR A 265 ARG 0.005 0.001 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 273 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.5981 (tptp) cc_final: 0.5748 (tptp) REVERT: A 71 MET cc_start: 0.7324 (mtm) cc_final: 0.7048 (mtp) REVERT: A 98 TYR cc_start: 0.6782 (t80) cc_final: 0.6243 (t80) REVERT: A 195 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8540 (pt) REVERT: A 213 LEU cc_start: 0.8444 (tp) cc_final: 0.8207 (tp) REVERT: A 629 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5912 (pt0) REVERT: A 735 ARG cc_start: 0.7895 (ppp80) cc_final: 0.7656 (ptm160) REVERT: A 777 ARG cc_start: 0.5944 (OUTLIER) cc_final: 0.5539 (ttt180) REVERT: B 150 ASP cc_start: 0.8039 (m-30) cc_final: 0.7814 (m-30) REVERT: C 90 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.6886 (ttp-110) REVERT: C 139 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8688 (m) REVERT: C 284 GLU cc_start: 0.5942 (mt-10) cc_final: 0.5709 (mt-10) REVERT: E 96 LEU cc_start: 0.8870 (tp) cc_final: 0.8621 (mt) REVERT: F 256 ASP cc_start: 0.7669 (t70) cc_final: 0.7410 (t70) REVERT: F 329 SER cc_start: 0.7141 (t) cc_final: 0.6772 (p) REVERT: F 341 TRP cc_start: 0.8381 (t60) cc_final: 0.8139 (t60) outliers start: 63 outliers final: 45 residues processed: 314 average time/residue: 0.3487 time to fit residues: 157.5082 Evaluate side-chains 307 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 258 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 208 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 186 optimal weight: 0.0870 chunk 56 optimal weight: 0.5980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN C 177 GLN D 199 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18127 Z= 0.178 Angle : 0.554 10.440 24726 Z= 0.282 Chirality : 0.042 0.153 2729 Planarity : 0.004 0.048 3031 Dihedral : 14.595 173.423 3104 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.57 % Allowed : 13.41 % Favored : 84.01 % 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: -2.10 (0.17), residues: 2127 helix: -0.73 (0.17), residues: 833 sheet: -1.36 (0.30), residues: 285 loop : -1.94 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 206 HIS 0.004 0.001 HIS A 61 PHE 0.021 0.001 PHE F 288 TYR 0.015 0.001 TYR B 125 ARG 0.006 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 273 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7702 (mmm-85) REVERT: A 39 ARG cc_start: 0.7499 (mtp85) cc_final: 0.7044 (mtm-85) REVERT: A 98 TYR cc_start: 0.6773 (t80) cc_final: 0.6203 (t80) REVERT: A 195 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8522 (pt) REVERT: A 213 LEU cc_start: 0.8490 (tp) cc_final: 0.8211 (tp) REVERT: A 629 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5874 (pt0) REVERT: A 735 ARG cc_start: 0.7827 (ppp80) cc_final: 0.7610 (ptm160) REVERT: A 777 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.5373 (ttt180) REVERT: C 90 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.6551 (ttp-110) REVERT: C 284 GLU cc_start: 0.6030 (mt-10) cc_final: 0.5744 (mt-10) REVERT: E 96 LEU cc_start: 0.8806 (tp) cc_final: 0.8574 (mt) REVERT: E 104 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8645 (tt) REVERT: F 200 GLU cc_start: 0.7389 (tt0) cc_final: 0.7014 (tt0) REVERT: F 256 ASP cc_start: 0.7623 (t70) cc_final: 0.7366 (t70) REVERT: F 285 PHE cc_start: 0.8316 (t80) cc_final: 0.7989 (t80) REVERT: F 329 SER cc_start: 0.7250 (t) cc_final: 0.6903 (p) REVERT: F 341 TRP cc_start: 0.8296 (t60) cc_final: 0.7888 (t60) outliers start: 43 outliers final: 30 residues processed: 300 average time/residue: 0.3609 time to fit residues: 158.7594 Evaluate side-chains 280 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 246 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 0.0870 chunk 178 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN D 83 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18127 Z= 0.324 Angle : 0.619 10.952 24726 Z= 0.315 Chirality : 0.046 0.172 2729 Planarity : 0.005 0.050 3031 Dihedral : 14.628 174.740 3104 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.83 % Allowed : 14.25 % Favored : 81.92 % 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: -1.92 (0.17), residues: 2127 helix: -0.46 (0.18), residues: 836 sheet: -1.47 (0.28), residues: 307 loop : -1.89 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 95 HIS 0.006 0.001 HIS D 205 PHE 0.030 0.002 PHE F 288 TYR 0.016 0.002 TYR A 265 ARG 0.008 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 257 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8047 (tp30) cc_final: 0.7766 (tp30) REVERT: A 87 MET cc_start: 0.7569 (tpp) cc_final: 0.6955 (mtp) REVERT: A 142 VAL cc_start: 0.8759 (t) cc_final: 0.8528 (m) REVERT: A 195 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8606 (pt) REVERT: A 629 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5965 (pt0) REVERT: C 90 ARG cc_start: 0.7372 (ttm-80) cc_final: 0.6777 (ttp-110) REVERT: C 284 GLU cc_start: 0.6128 (mt-10) cc_final: 0.5812 (mt-10) REVERT: D 160 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: E 96 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8668 (mt) REVERT: E 104 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8635 (tt) REVERT: F 200 GLU cc_start: 0.7454 (tt0) cc_final: 0.6939 (tt0) REVERT: F 256 ASP cc_start: 0.7736 (t70) cc_final: 0.7471 (t70) REVERT: F 329 SER cc_start: 0.7349 (t) cc_final: 0.6951 (p) outliers start: 64 outliers final: 45 residues processed: 299 average time/residue: 0.3616 time to fit residues: 155.1445 Evaluate side-chains 298 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 248 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN C 177 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18127 Z= 0.211 Angle : 0.562 10.669 24726 Z= 0.285 Chirality : 0.043 0.150 2729 Planarity : 0.004 0.050 3031 Dihedral : 14.544 174.211 3104 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.23 % Allowed : 15.21 % Favored : 81.56 % 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: -1.69 (0.18), residues: 2127 helix: -0.20 (0.18), residues: 838 sheet: -1.31 (0.30), residues: 286 loop : -1.84 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 95 HIS 0.004 0.001 HIS D 205 PHE 0.024 0.001 PHE F 288 TYR 0.014 0.001 TYR F 297 ARG 0.013 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 259 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7716 (tp30) cc_final: 0.6826 (tp30) REVERT: A 142 VAL cc_start: 0.8773 (t) cc_final: 0.8564 (m) REVERT: A 195 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8544 (pt) REVERT: A 237 GLU cc_start: 0.7785 (tt0) cc_final: 0.7459 (tt0) REVERT: A 629 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5939 (pt0) REVERT: A 707 TRP cc_start: 0.7269 (m100) cc_final: 0.7045 (m100) REVERT: A 777 ARG cc_start: 0.5696 (OUTLIER) cc_final: 0.5376 (ttt180) REVERT: C 90 ARG cc_start: 0.7200 (ttm-80) cc_final: 0.6375 (ttp-110) REVERT: C 195 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7007 (tp30) REVERT: C 284 GLU cc_start: 0.6231 (mt-10) cc_final: 0.5933 (mt-10) REVERT: D 160 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: E 96 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8638 (mt) REVERT: F 200 GLU cc_start: 0.7419 (tt0) cc_final: 0.6895 (tt0) REVERT: F 256 ASP cc_start: 0.7698 (t70) cc_final: 0.7436 (t70) REVERT: F 285 PHE cc_start: 0.8309 (t80) cc_final: 0.7934 (t80) REVERT: F 329 SER cc_start: 0.7239 (t) cc_final: 0.6893 (p) REVERT: F 341 TRP cc_start: 0.8360 (t60) cc_final: 0.7841 (t60) outliers start: 54 outliers final: 41 residues processed: 296 average time/residue: 0.3429 time to fit residues: 148.2858 Evaluate side-chains 294 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 247 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 119 optimal weight: 0.0870 chunk 152 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18127 Z= 0.164 Angle : 0.535 10.200 24726 Z= 0.270 Chirality : 0.042 0.151 2729 Planarity : 0.004 0.044 3031 Dihedral : 14.427 174.168 3104 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.75 % Allowed : 15.87 % Favored : 81.38 % 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: -1.44 (0.18), residues: 2127 helix: 0.03 (0.18), residues: 850 sheet: -1.26 (0.30), residues: 286 loop : -1.71 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 95 HIS 0.004 0.001 HIS A 61 PHE 0.022 0.001 PHE F 288 TYR 0.015 0.001 TYR F 297 ARG 0.009 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 264 time to evaluate : 1.940 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7930 (tp30) cc_final: 0.7121 (tp30) REVERT: A 87 MET cc_start: 0.7614 (tpp) cc_final: 0.6693 (mtp) REVERT: A 142 VAL cc_start: 0.8734 (t) cc_final: 0.8526 (m) REVERT: A 195 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8535 (pt) REVERT: A 237 GLU cc_start: 0.7736 (tt0) cc_final: 0.7428 (tt0) REVERT: A 245 ASP cc_start: 0.7800 (p0) cc_final: 0.7590 (p0) REVERT: A 629 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5943 (pt0) REVERT: A 707 TRP cc_start: 0.7301 (m100) cc_final: 0.7079 (m100) REVERT: A 777 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5276 (ttt180) REVERT: B 124 ARG cc_start: 0.7983 (ttt-90) cc_final: 0.7303 (mtp180) REVERT: B 150 ASP cc_start: 0.7997 (m-30) cc_final: 0.7442 (m-30) REVERT: C 90 ARG cc_start: 0.7244 (ttm-80) cc_final: 0.6368 (ttp-110) REVERT: C 284 GLU cc_start: 0.6388 (mt-10) cc_final: 0.6054 (mt-10) REVERT: D 160 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: E 96 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8575 (mt) REVERT: F 37 THR cc_start: 0.8189 (p) cc_final: 0.7922 (p) REVERT: F 39 ARG cc_start: 0.5782 (tmt170) cc_final: 0.4958 (tmm160) REVERT: F 109 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6789 (mtm110) REVERT: F 200 GLU cc_start: 0.7347 (tt0) cc_final: 0.6891 (tt0) REVERT: F 256 ASP cc_start: 0.7663 (t70) cc_final: 0.7396 (t70) REVERT: F 285 PHE cc_start: 0.8218 (t80) cc_final: 0.7879 (t80) REVERT: F 329 SER cc_start: 0.7015 (t) cc_final: 0.6727 (p) REVERT: F 341 TRP cc_start: 0.8277 (t60) cc_final: 0.7907 (t60) outliers start: 46 outliers final: 33 residues processed: 298 average time/residue: 0.3344 time to fit residues: 144.8917 Evaluate side-chains 287 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 248 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 HIS C 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18127 Z= 0.173 Angle : 0.534 10.527 24726 Z= 0.270 Chirality : 0.042 0.150 2729 Planarity : 0.004 0.044 3031 Dihedral : 14.386 174.479 3104 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.87 % Allowed : 15.81 % Favored : 81.32 % 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: -1.22 (0.18), residues: 2127 helix: 0.22 (0.19), residues: 844 sheet: -1.22 (0.29), residues: 292 loop : -1.56 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 95 HIS 0.003 0.001 HIS A 61 PHE 0.021 0.001 PHE F 288 TYR 0.015 0.001 TYR F 297 ARG 0.008 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 267 time to evaluate : 1.985 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7752 (tp30) cc_final: 0.6976 (tp30) REVERT: A 62 LYS cc_start: 0.6012 (tptp) cc_final: 0.5279 (ttpp) REVERT: A 142 VAL cc_start: 0.8723 (t) cc_final: 0.8507 (m) REVERT: A 195 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8527 (pt) REVERT: A 237 GLU cc_start: 0.7738 (tt0) cc_final: 0.7434 (tt0) REVERT: A 245 ASP cc_start: 0.7802 (p0) cc_final: 0.7592 (p0) REVERT: A 601 GLU cc_start: 0.7345 (tt0) cc_final: 0.7115 (tt0) REVERT: A 629 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5953 (pt0) REVERT: A 707 TRP cc_start: 0.7287 (m100) cc_final: 0.7075 (m100) REVERT: A 777 ARG cc_start: 0.5599 (OUTLIER) cc_final: 0.5257 (ttt180) REVERT: B 73 LYS cc_start: 0.6524 (tttm) cc_final: 0.6252 (tttm) REVERT: C 75 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7446 (mtm110) REVERT: C 90 ARG cc_start: 0.7197 (ttm-80) cc_final: 0.6311 (ttp-110) REVERT: C 195 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7121 (tp30) REVERT: C 257 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6532 (tp30) REVERT: C 284 GLU cc_start: 0.6352 (mt-10) cc_final: 0.6017 (mt-10) REVERT: D 160 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: E 96 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8586 (mt) REVERT: F 37 THR cc_start: 0.8077 (p) cc_final: 0.7816 (p) REVERT: F 39 ARG cc_start: 0.5682 (tmt170) cc_final: 0.4845 (tmm160) REVERT: F 109 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6798 (mtm110) REVERT: F 200 GLU cc_start: 0.7330 (tt0) cc_final: 0.6937 (tt0) REVERT: F 256 ASP cc_start: 0.7655 (t70) cc_final: 0.7375 (t70) REVERT: F 285 PHE cc_start: 0.8223 (t80) cc_final: 0.7881 (t80) REVERT: F 329 SER cc_start: 0.7036 (t) cc_final: 0.6722 (p) REVERT: F 341 TRP cc_start: 0.8300 (t60) cc_final: 0.7939 (t60) outliers start: 48 outliers final: 35 residues processed: 302 average time/residue: 0.3403 time to fit residues: 148.7524 Evaluate side-chains 295 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 252 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18127 Z= 0.329 Angle : 0.621 10.987 24726 Z= 0.312 Chirality : 0.046 0.247 2729 Planarity : 0.004 0.047 3031 Dihedral : 14.461 174.429 3104 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.23 % Allowed : 15.75 % Favored : 81.02 % 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: -1.29 (0.18), residues: 2127 helix: 0.15 (0.19), residues: 841 sheet: -1.21 (0.30), residues: 292 loop : -1.61 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 95 HIS 0.005 0.001 HIS D 205 PHE 0.023 0.002 PHE F 288 TYR 0.030 0.002 TYR A 552 ARG 0.008 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 252 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8006 (tp30) cc_final: 0.7531 (tp30) REVERT: A 142 VAL cc_start: 0.8704 (t) cc_final: 0.8500 (m) REVERT: A 195 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8582 (pt) REVERT: A 237 GLU cc_start: 0.7732 (tt0) cc_final: 0.7407 (tt0) REVERT: A 629 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6126 (pt0) REVERT: A 707 TRP cc_start: 0.7344 (m100) cc_final: 0.7136 (m100) REVERT: A 777 ARG cc_start: 0.5685 (OUTLIER) cc_final: 0.5338 (ttt180) REVERT: C 90 ARG cc_start: 0.7113 (ttm-80) cc_final: 0.6425 (ttp80) REVERT: C 195 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7073 (tp30) REVERT: C 284 GLU cc_start: 0.6449 (mt-10) cc_final: 0.6109 (mt-10) REVERT: D 160 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: E 96 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8572 (mt) REVERT: F 200 GLU cc_start: 0.7453 (tt0) cc_final: 0.6946 (tt0) REVERT: F 285 PHE cc_start: 0.8402 (t80) cc_final: 0.8039 (t80) REVERT: F 329 SER cc_start: 0.6963 (t) cc_final: 0.6655 (p) outliers start: 54 outliers final: 44 residues processed: 287 average time/residue: 0.3289 time to fit residues: 139.4796 Evaluate side-chains 290 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 240 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18127 Z= 0.218 Angle : 0.576 10.754 24726 Z= 0.289 Chirality : 0.043 0.196 2729 Planarity : 0.004 0.043 3031 Dihedral : 14.411 173.939 3104 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.87 % Allowed : 16.59 % Favored : 80.54 % 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: -1.18 (0.18), residues: 2127 helix: 0.25 (0.19), residues: 843 sheet: -1.14 (0.30), residues: 290 loop : -1.55 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 95 HIS 0.007 0.001 HIS A 295 PHE 0.019 0.001 PHE F 288 TYR 0.022 0.001 TYR A 552 ARG 0.007 0.001 ARG D 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 248 time to evaluate : 2.064 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.5896 (tptp) cc_final: 0.5600 (ttpp) REVERT: A 195 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8564 (pt) REVERT: A 237 GLU cc_start: 0.7742 (tt0) cc_final: 0.7481 (tt0) REVERT: A 629 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.6010 (pt0) REVERT: A 707 TRP cc_start: 0.7306 (m100) cc_final: 0.7090 (m100) REVERT: A 777 ARG cc_start: 0.5603 (OUTLIER) cc_final: 0.5304 (ttt180) REVERT: B 150 ASP cc_start: 0.7770 (m-30) cc_final: 0.7130 (t0) REVERT: B 154 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6686 (mm-30) REVERT: C 75 ARG cc_start: 0.7730 (mtm110) cc_final: 0.7493 (mtm110) REVERT: C 90 ARG cc_start: 0.7190 (ttm-80) cc_final: 0.6305 (ttp-110) REVERT: C 195 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: C 284 GLU cc_start: 0.6391 (mt-10) cc_final: 0.6045 (mt-10) REVERT: D 160 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: E 96 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8573 (mt) REVERT: F 39 ARG cc_start: 0.5214 (tmt170) cc_final: 0.4668 (ttp-170) REVERT: F 200 GLU cc_start: 0.7428 (tt0) cc_final: 0.6937 (tt0) REVERT: F 285 PHE cc_start: 0.8362 (t80) cc_final: 0.7988 (t80) REVERT: F 329 SER cc_start: 0.6913 (t) cc_final: 0.6615 (p) outliers start: 48 outliers final: 41 residues processed: 281 average time/residue: 0.3253 time to fit residues: 134.9869 Evaluate side-chains 289 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 242 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 8.9990 chunk 52 optimal weight: 0.1980 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.165784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132019 restraints weight = 24197.094| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.16 r_work: 0.3293 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18127 Z= 0.174 Angle : 0.551 10.489 24726 Z= 0.276 Chirality : 0.042 0.152 2729 Planarity : 0.004 0.044 3031 Dihedral : 14.342 173.873 3102 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.69 % Allowed : 17.07 % Favored : 80.24 % 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: -1.04 (0.18), residues: 2127 helix: 0.39 (0.19), residues: 847 sheet: -1.08 (0.30), residues: 282 loop : -1.50 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 95 HIS 0.006 0.001 HIS A 295 PHE 0.018 0.001 PHE F 288 TYR 0.018 0.001 TYR F 297 ARG 0.007 0.000 ARG A 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4116.59 seconds wall clock time: 75 minutes 22.79 seconds (4522.79 seconds total)