Starting phenix.real_space_refine on Tue Dec 31 05:57:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sc5_25022/12_2024/7sc5_25022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sc5_25022/12_2024/7sc5_25022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sc5_25022/12_2024/7sc5_25022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sc5_25022/12_2024/7sc5_25022.map" model { file = "/net/cci-nas-00/data/ceres_data/7sc5_25022/12_2024/7sc5_25022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sc5_25022/12_2024/7sc5_25022.cif" } resolution = 3.88 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= 0.001 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: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9192 2.51 5 N 2511 2.21 5 O 2901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14703 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "B" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "D" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "F" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.97, per 1000 atoms: 0.68 Number of scatterers: 14703 At special positions: 0 Unit cell: (122.57, 130.81, 129.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2901 8.00 N 2511 7.00 C 9192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 330 " distance=2.02 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 443 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 330 " distance=2.02 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 443 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 330 " distance=2.02 Simple disulfide: pdb=" SG CYS E 377 " - pdb=" SG CYS E 443 " distance=2.03 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=3, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 152 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 331 " " NAG A 605 " - " ASN A 446 " " NAG A 606 " - " ASN A 391 " " NAG A 607 " - " ASN A 385 " " NAG A 608 " - " ASN A 88 " " NAG A 609 " - " ASN A 148 " " NAG B 801 " - " ASN B 625 " " NAG B 802 " - " ASN B 618 " " NAG B 803 " - " ASN B 637 " " NAG C 601 " - " ASN C 152 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 331 " " NAG C 605 " - " ASN C 446 " " NAG C 606 " - " ASN C 391 " " NAG C 607 " - " ASN C 385 " " NAG C 608 " - " ASN C 88 " " NAG C 609 " - " ASN C 148 " " NAG D 801 " - " ASN D 625 " " NAG D 802 " - " ASN D 618 " " NAG D 803 " - " ASN D 637 " " NAG E 601 " - " ASN E 152 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 331 " " NAG E 605 " - " ASN E 446 " " NAG E 606 " - " ASN E 391 " " NAG E 607 " - " ASN E 385 " " NAG E 608 " - " ASN E 88 " " NAG E 609 " - " ASN E 148 " " NAG F 801 " - " ASN F 625 " " NAG F 802 " - " ASN F 618 " " NAG F 803 " - " ASN F 637 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 354 " " NAG K 1 " - " ASN C 234 " " NAG L 1 " - " ASN C 354 " " NAG N 1 " - " ASN E 234 " " NAG O 1 " - " ASN E 354 " NAG-SER " NAG G 1 " - " SER A 445 " " NAG J 1 " - " SER C 445 " " NAG M 1 " - " SER E 445 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.24 Conformation dependent library (CDL) restraints added in 1.9 seconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 27 sheets defined 24.4% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.972A pdb=" N LYS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.936A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.694A pdb=" N GLN B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.085A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 652 removed outlier: 4.087A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 660 Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 333 through 352 removed outlier: 3.972A pdb=" N LYS C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS C 351 " --> pdb=" O GLN C 347 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.937A pdb=" N TRP C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 539 Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.693A pdb=" N GLN D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 Processing helix chain 'D' and resid 570 through 596 removed outlier: 4.086A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN D 590 " --> pdb=" O TYR D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 652 removed outlier: 4.087A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 660 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 333 through 352 removed outlier: 3.971A pdb=" N LYS E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE E 352 " --> pdb=" O LEU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.558A pdb=" N THR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 479 removed outlier: 3.937A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 539 Processing helix chain 'F' and resid 540 through 542 No H-bonds generated for 'chain 'F' and resid 540 through 542' Processing helix chain 'F' and resid 543 through 551 removed outlier: 3.693A pdb=" N GLN F 551 " --> pdb=" O GLY F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 558 Processing helix chain 'F' and resid 570 through 596 removed outlier: 4.085A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 652 removed outlier: 4.085A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 660 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 6.264A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE A 151 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.823A pdb=" N LEU A 260 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU A 450 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 441 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 445 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 328 " --> pdb=" O CYS A 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 421 through 423 Processing sheet with id=AB1, first strand: chain 'C' and resid 492 through 497 removed outlier: 6.107A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS D 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB4, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE C 151 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.824A pdb=" N LEU C 260 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU C 450 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 441 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER C 445 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C 328 " --> pdb=" O CYS C 416 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 421 through 423 Processing sheet with id=AC1, first strand: chain 'E' and resid 492 through 497 removed outlier: 6.204A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS F 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE E 151 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 173 through 174 Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.823A pdb=" N LEU E 260 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU E 450 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 441 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER E 445 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA E 328 " --> pdb=" O CYS E 416 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'E' and resid 421 through 423 441 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4603 1.34 - 1.46: 3045 1.46 - 1.57: 7190 1.57 - 1.69: 3 1.69 - 1.81: 132 Bond restraints: 14973 Sorted by residual: bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.335 1.376 -0.041 9.40e-03 1.13e+04 1.88e+01 bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.335 1.375 -0.040 9.40e-03 1.13e+04 1.83e+01 bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.335 1.375 -0.040 9.40e-03 1.13e+04 1.80e+01 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.594 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.593 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 14968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 19425 2.35 - 4.69: 731 4.69 - 7.04: 136 7.04 - 9.39: 24 9.39 - 11.74: 15 Bond angle restraints: 20331 Sorted by residual: angle pdb=" C MET E 153 " pdb=" N THR E 154 " pdb=" CA THR E 154 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C MET C 153 " pdb=" N THR C 154 " pdb=" CA THR C 154 " ideal model delta sigma weight residual 121.54 133.26 -11.72 1.91e+00 2.74e-01 3.77e+01 angle pdb=" C MET A 153 " pdb=" N THR A 154 " pdb=" CA THR A 154 " ideal model delta sigma weight residual 121.54 133.23 -11.69 1.91e+00 2.74e-01 3.75e+01 angle pdb=" CA SER F 612 " pdb=" C SER F 612 " pdb=" O SER F 612 " ideal model delta sigma weight residual 118.91 109.69 9.22 1.60e+00 3.91e-01 3.32e+01 angle pdb=" CA SER D 612 " pdb=" C SER D 612 " pdb=" O SER D 612 " ideal model delta sigma weight residual 118.91 109.73 9.18 1.60e+00 3.91e-01 3.29e+01 ... (remaining 20326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.33: 9048 22.33 - 44.66: 582 44.66 - 66.99: 117 66.99 - 89.32: 63 89.32 - 111.65: 24 Dihedral angle restraints: 9834 sinusoidal: 4719 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 172.34 -79.34 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 172.32 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 172.31 -79.31 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 9831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2344 0.114 - 0.227: 119 0.227 - 0.341: 9 0.341 - 0.455: 15 0.455 - 0.568: 3 Chirality restraints: 2490 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 7.98e+00 ... (remaining 2487 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 609 " -0.265 2.00e-02 2.50e+03 2.22e-01 6.13e+02 pdb=" C7 NAG E 609 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG E 609 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG E 609 " 0.371 2.00e-02 2.50e+03 pdb=" O7 NAG E 609 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 609 " -0.256 2.00e-02 2.50e+03 2.14e-01 5.71e+02 pdb=" C7 NAG C 609 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG C 609 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG C 609 " 0.357 2.00e-02 2.50e+03 pdb=" O7 NAG C 609 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 609 " -0.242 2.00e-02 2.50e+03 2.01e-01 5.07e+02 pdb=" C7 NAG A 609 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 609 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A 609 " 0.334 2.00e-02 2.50e+03 pdb=" O7 NAG A 609 " 0.012 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 230 2.55 - 3.14: 11369 3.14 - 3.72: 23109 3.72 - 4.31: 30743 4.31 - 4.90: 48887 Nonbonded interactions: 114338 Sorted by model distance: nonbonded pdb=" O ASP C 367 " pdb=" N GLU C 369 " model vdw 1.959 3.120 nonbonded pdb=" O3 NAG A 609 " pdb=" O7 NAG A 609 " model vdw 2.053 3.040 nonbonded pdb=" O3 NAG C 609 " pdb=" O7 NAG C 609 " model vdw 2.060 3.040 nonbonded pdb=" O3 NAG E 609 " pdb=" O7 NAG E 609 " model vdw 2.070 3.040 nonbonded pdb=" ND2 ASN E 362 " pdb=" O THR E 371 " model vdw 2.196 3.120 ... (remaining 114333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.890 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: 0.060 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 37.740 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 0.075 14973 Z= 0.503 Angle : 1.108 11.737 20331 Z= 0.592 Chirality : 0.070 0.568 2490 Planarity : 0.009 0.222 2520 Dihedral : 17.367 111.646 6420 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.30 % Favored : 88.47 % Rotamer: Outliers : 0.97 % Allowed : 7.52 % Favored : 91.50 % 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: -5.17 (0.16), residues: 1734 helix: -3.87 (0.12), residues: 405 sheet: -2.56 (0.22), residues: 474 loop : -3.75 (0.17), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 394 HIS 0.010 0.002 HIS C 373 PHE 0.013 0.002 PHE A 93 TYR 0.015 0.002 TYR C 165 ARG 0.007 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.5687 (ttt) cc_final: 0.4003 (ttm) REVERT: B 567 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7901 (mmtm) REVERT: B 601 LYS cc_start: 0.9086 (mtmm) cc_final: 0.8587 (mtmm) REVERT: B 632 GLU cc_start: 0.9367 (tp30) cc_final: 0.9082 (tp30) REVERT: B 651 ASN cc_start: 0.9048 (t0) cc_final: 0.8822 (t0) REVERT: B 657 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8777 (mt-10) REVERT: C 69 TRP cc_start: 0.9256 (m-90) cc_final: 0.8715 (m-90) REVERT: C 424 MET cc_start: 0.5931 (ttt) cc_final: 0.4315 (ttm) REVERT: C 447 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9249 (mp) REVERT: D 601 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8465 (mtmm) REVERT: D 632 GLU cc_start: 0.9328 (tp30) cc_final: 0.8966 (tp30) REVERT: D 657 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8691 (mt-10) REVERT: E 69 TRP cc_start: 0.9174 (m-90) cc_final: 0.8696 (m-90) REVERT: E 264 SER cc_start: 0.9099 (t) cc_final: 0.8761 (m) REVERT: F 601 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8271 (mtmm) REVERT: F 632 GLU cc_start: 0.9287 (tp30) cc_final: 0.8964 (tp30) REVERT: F 633 LYS cc_start: 0.9730 (mttt) cc_final: 0.9481 (mttp) REVERT: F 651 ASN cc_start: 0.9097 (t0) cc_final: 0.8681 (t0) REVERT: F 657 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8728 (mt-10) outliers start: 15 outliers final: 9 residues processed: 194 average time/residue: 0.3282 time to fit residues: 90.2354 Evaluate side-chains 120 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 138 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 295 ASN A 300 ASN A 373 HIS B 550 GLN B 551 GLN B 564 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN C 276 ASN C 295 ASN C 300 ASN C 373 HIS D 550 GLN D 551 GLN D 564 HIS D 656 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 ASN E 295 ASN E 300 ASN E 373 HIS F 550 GLN F 551 GLN F 564 HIS F 575 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14973 Z= 0.241 Angle : 0.820 9.999 20331 Z= 0.406 Chirality : 0.053 0.339 2490 Planarity : 0.004 0.041 2520 Dihedral : 13.501 81.242 3132 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 2.53 % Allowed : 11.35 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.86 (0.18), residues: 1734 helix: -1.71 (0.21), residues: 414 sheet: -2.05 (0.23), residues: 444 loop : -3.33 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 394 HIS 0.005 0.001 HIS B 564 PHE 0.010 0.001 PHE C 93 TYR 0.017 0.002 TYR C 383 ARG 0.011 0.001 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8940 (pp) REVERT: B 632 GLU cc_start: 0.9304 (tp30) cc_final: 0.9008 (tp30) REVERT: B 651 ASN cc_start: 0.9049 (t0) cc_final: 0.8699 (t0) REVERT: B 657 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8743 (mt-10) REVERT: C 69 TRP cc_start: 0.9257 (m-90) cc_final: 0.8682 (m-90) REVERT: C 271 MET cc_start: 0.8720 (mmm) cc_final: 0.8378 (mmm) REVERT: D 530 MET cc_start: 0.6994 (mtm) cc_final: 0.6740 (mtm) REVERT: D 574 LYS cc_start: 0.9159 (mmmt) cc_final: 0.8848 (ptmt) REVERT: D 601 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8400 (mtmm) REVERT: D 626 MET cc_start: 0.8639 (ttm) cc_final: 0.8400 (ttm) REVERT: D 632 GLU cc_start: 0.9282 (tp30) cc_final: 0.8935 (tp30) REVERT: D 657 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8670 (mt-10) REVERT: E 69 TRP cc_start: 0.9171 (m-90) cc_final: 0.8623 (m-90) REVERT: E 260 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9116 (pp) REVERT: E 264 SER cc_start: 0.9118 (t) cc_final: 0.8804 (m) REVERT: E 424 MET cc_start: 0.5904 (ttt) cc_final: 0.4739 (ttm) REVERT: F 601 LYS cc_start: 0.8669 (mtmm) cc_final: 0.8025 (mtmm) REVERT: F 632 GLU cc_start: 0.9185 (tp30) cc_final: 0.8900 (tp30) REVERT: F 633 LYS cc_start: 0.9725 (mttt) cc_final: 0.9503 (mttp) REVERT: F 651 ASN cc_start: 0.9165 (t0) cc_final: 0.8857 (t0) REVERT: F 654 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8075 (tm-30) REVERT: F 657 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8712 (mt-10) outliers start: 39 outliers final: 17 residues processed: 162 average time/residue: 0.2672 time to fit residues: 63.8293 Evaluate side-chains 135 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN E 82 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 14973 Z= 0.477 Angle : 0.895 9.569 20331 Z= 0.444 Chirality : 0.053 0.280 2490 Planarity : 0.005 0.078 2520 Dihedral : 11.774 64.341 3129 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.49 % Favored : 86.33 % Rotamer: Outliers : 3.96 % Allowed : 15.11 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.22 (0.19), residues: 1734 helix: -0.46 (0.25), residues: 399 sheet: -2.11 (0.22), residues: 438 loop : -3.02 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 477 HIS 0.008 0.002 HIS A 373 PHE 0.024 0.002 PHE E 360 TYR 0.010 0.002 TYR C 484 ARG 0.013 0.001 ARG E 427 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 120 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8965 (pp) REVERT: B 651 ASN cc_start: 0.9257 (t0) cc_final: 0.8997 (t0) REVERT: B 657 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8777 (mt-10) REVERT: C 69 TRP cc_start: 0.9250 (m-90) cc_final: 0.8632 (m-90) REVERT: D 530 MET cc_start: 0.7651 (mtm) cc_final: 0.7146 (mtm) REVERT: D 574 LYS cc_start: 0.9294 (mmmt) cc_final: 0.9034 (ptmt) REVERT: D 601 LYS cc_start: 0.8906 (mtmm) cc_final: 0.8563 (mtmm) REVERT: D 626 MET cc_start: 0.8650 (ttm) cc_final: 0.8258 (ttm) REVERT: D 632 GLU cc_start: 0.9311 (tp30) cc_final: 0.9058 (tp30) REVERT: D 657 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8668 (mt-10) REVERT: E 69 TRP cc_start: 0.9192 (m-90) cc_final: 0.8579 (m-90) REVERT: E 264 SER cc_start: 0.9258 (t) cc_final: 0.8849 (m) REVERT: E 424 MET cc_start: 0.6469 (ttt) cc_final: 0.6168 (ttm) REVERT: F 530 MET cc_start: 0.7909 (mtm) cc_final: 0.7709 (mtm) REVERT: F 601 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8214 (mtmm) REVERT: F 633 LYS cc_start: 0.9703 (mttt) cc_final: 0.9491 (mttp) REVERT: F 651 ASN cc_start: 0.9223 (t0) cc_final: 0.8858 (t0) REVERT: F 654 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8517 (tm-30) REVERT: F 657 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8733 (mt-10) outliers start: 61 outliers final: 35 residues processed: 169 average time/residue: 0.2923 time to fit residues: 73.0396 Evaluate side-chains 142 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 195 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN B 575 GLN C 82 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14973 Z= 0.192 Angle : 0.747 9.557 20331 Z= 0.367 Chirality : 0.051 0.317 2490 Planarity : 0.004 0.069 2520 Dihedral : 10.359 59.582 3125 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.65 % Favored : 88.29 % Rotamer: Outliers : 2.59 % Allowed : 18.03 % Favored : 79.38 % 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: -2.97 (0.19), residues: 1734 helix: -0.26 (0.26), residues: 402 sheet: -1.82 (0.23), residues: 429 loop : -2.95 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 571 HIS 0.002 0.001 HIS D 564 PHE 0.023 0.001 PHE E 360 TYR 0.008 0.001 TYR A 383 ARG 0.007 0.001 ARG F 557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8841 (pp) REVERT: B 626 MET cc_start: 0.8445 (ttm) cc_final: 0.8123 (ttm) REVERT: B 651 ASN cc_start: 0.9137 (t0) cc_final: 0.8873 (t0) REVERT: B 657 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8738 (mt-10) REVERT: C 69 TRP cc_start: 0.9297 (m-90) cc_final: 0.8921 (m-90) REVERT: C 104 MET cc_start: 0.9181 (ttt) cc_final: 0.8931 (ttp) REVERT: C 113 ASP cc_start: 0.9169 (m-30) cc_final: 0.8935 (m-30) REVERT: C 271 MET cc_start: 0.8508 (tpt) cc_final: 0.8262 (tmm) REVERT: D 530 MET cc_start: 0.6988 (mtm) cc_final: 0.6452 (mtm) REVERT: D 574 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8990 (ptmt) REVERT: D 601 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8403 (mtmm) REVERT: D 626 MET cc_start: 0.8617 (ttm) cc_final: 0.8188 (ttm) REVERT: D 632 GLU cc_start: 0.9296 (tp30) cc_final: 0.9057 (tp30) REVERT: D 633 LYS cc_start: 0.9639 (mttm) cc_final: 0.9302 (mttp) REVERT: D 657 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8629 (mt-10) REVERT: E 69 TRP cc_start: 0.9155 (m-90) cc_final: 0.8647 (m-90) REVERT: E 264 SER cc_start: 0.9117 (t) cc_final: 0.8736 (m) REVERT: E 424 MET cc_start: 0.6467 (ttt) cc_final: 0.5781 (ttm) REVERT: F 530 MET cc_start: 0.7372 (mtm) cc_final: 0.7080 (mtm) REVERT: F 544 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8341 (mp) REVERT: F 633 LYS cc_start: 0.9693 (mttt) cc_final: 0.9470 (mttp) REVERT: F 651 ASN cc_start: 0.9178 (t0) cc_final: 0.8865 (t0) REVERT: F 654 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8463 (tm-30) REVERT: F 657 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8709 (mt-10) outliers start: 40 outliers final: 30 residues processed: 165 average time/residue: 0.2885 time to fit residues: 69.2030 Evaluate side-chains 147 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 127 optimal weight: 0.0050 chunk 70 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 153 optimal weight: 0.0040 chunk 43 optimal weight: 3.9990 overall best weight: 3.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14973 Z= 0.352 Angle : 0.793 11.009 20331 Z= 0.392 Chirality : 0.051 0.276 2490 Planarity : 0.004 0.097 2520 Dihedral : 9.882 58.151 3124 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.67 % Favored : 86.16 % Rotamer: Outliers : 3.70 % Allowed : 18.61 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.97 (0.19), residues: 1734 helix: -0.02 (0.27), residues: 399 sheet: -1.85 (0.23), residues: 429 loop : -3.05 (0.18), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 571 HIS 0.004 0.001 HIS A 373 PHE 0.027 0.002 PHE E 360 TYR 0.007 0.001 TYR A 217 ARG 0.011 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 118 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8792 (pp) REVERT: B 651 ASN cc_start: 0.9194 (t0) cc_final: 0.8970 (t0) REVERT: B 657 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8804 (mt-10) REVERT: C 69 TRP cc_start: 0.9288 (m-90) cc_final: 0.8696 (m-90) REVERT: C 104 MET cc_start: 0.9250 (ttt) cc_final: 0.8933 (ttt) REVERT: D 530 MET cc_start: 0.7580 (mtm) cc_final: 0.7337 (mtm) REVERT: D 574 LYS cc_start: 0.9250 (mmmt) cc_final: 0.9008 (ptmt) REVERT: D 601 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8644 (mtpp) REVERT: D 632 GLU cc_start: 0.9298 (tp30) cc_final: 0.9056 (tp30) REVERT: D 654 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8044 (tm-30) REVERT: D 657 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8644 (mt-10) REVERT: E 69 TRP cc_start: 0.9144 (m-90) cc_final: 0.8567 (m-90) REVERT: F 633 LYS cc_start: 0.9693 (mttt) cc_final: 0.9478 (mttp) REVERT: F 651 ASN cc_start: 0.9221 (t0) cc_final: 0.8945 (t0) REVERT: F 654 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8422 (tm-30) REVERT: F 657 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8855 (mt-10) outliers start: 57 outliers final: 42 residues processed: 167 average time/residue: 0.2748 time to fit residues: 68.1576 Evaluate side-chains 151 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14973 Z= 0.228 Angle : 0.738 9.511 20331 Z= 0.366 Chirality : 0.050 0.280 2490 Planarity : 0.004 0.088 2520 Dihedral : 9.297 57.423 3124 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.94 % Favored : 87.89 % Rotamer: Outliers : 3.57 % Allowed : 20.10 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.82 (0.19), residues: 1734 helix: -0.20 (0.26), residues: 417 sheet: -1.52 (0.25), residues: 378 loop : -2.92 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 571 HIS 0.002 0.001 HIS D 564 PHE 0.037 0.001 PHE A 360 TYR 0.009 0.001 TYR A 217 ARG 0.006 0.000 ARG F 557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 123 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8721 (m-30) cc_final: 0.8461 (t0) REVERT: A 260 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8731 (pp) REVERT: B 651 ASN cc_start: 0.9149 (t0) cc_final: 0.8915 (t0) REVERT: B 657 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8751 (mt-10) REVERT: C 69 TRP cc_start: 0.9298 (m-90) cc_final: 0.8748 (m-90) REVERT: C 104 MET cc_start: 0.9211 (ttt) cc_final: 0.8956 (ttt) REVERT: C 113 ASP cc_start: 0.9162 (m-30) cc_final: 0.8919 (m-30) REVERT: D 530 MET cc_start: 0.7323 (mtm) cc_final: 0.7085 (mtm) REVERT: D 601 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8608 (mtpp) REVERT: D 632 GLU cc_start: 0.9274 (tp30) cc_final: 0.9052 (tp30) REVERT: D 633 LYS cc_start: 0.9635 (mttm) cc_final: 0.9301 (mttp) REVERT: D 657 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8609 (mt-10) REVERT: E 69 TRP cc_start: 0.9132 (m-90) cc_final: 0.8630 (m-90) REVERT: E 153 MET cc_start: 0.7399 (tpt) cc_final: 0.7117 (tpt) REVERT: F 530 MET cc_start: 0.7315 (mtm) cc_final: 0.7111 (mtm) REVERT: F 651 ASN cc_start: 0.9163 (t0) cc_final: 0.8909 (t0) REVERT: F 654 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8430 (tm-30) REVERT: F 657 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8726 (mt-10) outliers start: 55 outliers final: 40 residues processed: 170 average time/residue: 0.2648 time to fit residues: 67.8702 Evaluate side-chains 153 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 170 optimal weight: 0.2980 chunk 106 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14973 Z= 0.235 Angle : 0.735 9.647 20331 Z= 0.364 Chirality : 0.050 0.273 2490 Planarity : 0.004 0.080 2520 Dihedral : 8.968 57.354 3123 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.32 % Favored : 86.51 % Rotamer: Outliers : 3.57 % Allowed : 20.88 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.19), residues: 1734 helix: -0.19 (0.27), residues: 420 sheet: -1.64 (0.23), residues: 432 loop : -2.84 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 571 HIS 0.002 0.001 HIS E 351 PHE 0.039 0.002 PHE A 360 TYR 0.006 0.001 TYR D 643 ARG 0.008 0.000 ARG F 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 123 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8673 (m-30) cc_final: 0.8444 (t0) REVERT: A 260 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8743 (pp) REVERT: B 651 ASN cc_start: 0.9133 (t0) cc_final: 0.8905 (t0) REVERT: B 657 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8745 (mt-10) REVERT: C 69 TRP cc_start: 0.9288 (m-90) cc_final: 0.8752 (m-90) REVERT: C 113 ASP cc_start: 0.9163 (m-30) cc_final: 0.8924 (m-30) REVERT: C 432 MET cc_start: 0.8510 (ppp) cc_final: 0.8198 (tmm) REVERT: D 530 MET cc_start: 0.7349 (mtm) cc_final: 0.7107 (mtm) REVERT: D 633 LYS cc_start: 0.9640 (mttm) cc_final: 0.9291 (mttp) REVERT: D 657 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8629 (mt-10) REVERT: E 69 TRP cc_start: 0.9132 (m-90) cc_final: 0.8649 (m-90) REVERT: F 530 MET cc_start: 0.7234 (mtm) cc_final: 0.7009 (mtm) REVERT: F 601 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8700 (ptpp) REVERT: F 651 ASN cc_start: 0.9167 (t0) cc_final: 0.8908 (t0) REVERT: F 654 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8406 (tm-30) REVERT: F 657 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8810 (mt-10) outliers start: 55 outliers final: 46 residues processed: 169 average time/residue: 0.2755 time to fit residues: 69.4565 Evaluate side-chains 162 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 7.9990 chunk 68 optimal weight: 0.0370 chunk 101 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14973 Z= 0.206 Angle : 0.743 12.812 20331 Z= 0.367 Chirality : 0.049 0.279 2490 Planarity : 0.004 0.073 2520 Dihedral : 8.725 57.299 3121 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.48 % Favored : 88.35 % Rotamer: Outliers : 3.63 % Allowed : 21.08 % Favored : 75.29 % 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 (0.19), residues: 1734 helix: -0.17 (0.27), residues: 420 sheet: -1.39 (0.26), residues: 363 loop : -2.79 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 571 HIS 0.002 0.000 HIS D 564 PHE 0.032 0.001 PHE C 360 TYR 0.006 0.001 TYR C 316 ARG 0.011 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8685 (m-30) cc_final: 0.8387 (t0) REVERT: A 260 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8701 (pp) REVERT: B 651 ASN cc_start: 0.9112 (t0) cc_final: 0.8872 (t0) REVERT: B 654 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 657 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8724 (mt-10) REVERT: C 69 TRP cc_start: 0.9283 (m-90) cc_final: 0.8798 (m-90) REVERT: C 113 ASP cc_start: 0.9100 (m-30) cc_final: 0.8873 (m-30) REVERT: C 424 MET cc_start: 0.7566 (tmm) cc_final: 0.7225 (tmm) REVERT: C 447 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9252 (mp) REVERT: D 530 MET cc_start: 0.7260 (mtm) cc_final: 0.6868 (mtm) REVERT: D 601 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8281 (ptpp) REVERT: D 633 LYS cc_start: 0.9641 (mttm) cc_final: 0.9278 (mttp) REVERT: D 654 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7730 (tm-30) REVERT: D 657 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8638 (mt-10) REVERT: E 69 TRP cc_start: 0.9149 (m-90) cc_final: 0.8736 (m-90) REVERT: F 530 MET cc_start: 0.7135 (mtm) cc_final: 0.6888 (mtm) REVERT: F 601 LYS cc_start: 0.8846 (mtmm) cc_final: 0.8538 (ptpp) REVERT: F 651 ASN cc_start: 0.9115 (t0) cc_final: 0.8835 (t0) REVERT: F 654 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8407 (tm-30) REVERT: F 657 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8836 (mt-10) outliers start: 56 outliers final: 47 residues processed: 166 average time/residue: 0.2631 time to fit residues: 66.8560 Evaluate side-chains 163 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 ARG Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 104 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14973 Z= 0.210 Angle : 0.745 11.129 20331 Z= 0.367 Chirality : 0.049 0.282 2490 Planarity : 0.004 0.068 2520 Dihedral : 8.552 57.321 3121 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.40 % Favored : 87.43 % Rotamer: Outliers : 3.83 % Allowed : 21.34 % Favored : 74.84 % 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: -2.60 (0.20), residues: 1734 helix: -0.21 (0.27), residues: 426 sheet: -1.37 (0.26), residues: 363 loop : -2.71 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 571 HIS 0.002 0.001 HIS D 564 PHE 0.028 0.001 PHE C 360 TYR 0.006 0.001 TYR A 316 ARG 0.016 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 124 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8687 (m-30) cc_final: 0.8397 (t0) REVERT: A 260 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8688 (pp) REVERT: B 651 ASN cc_start: 0.8782 (t0) cc_final: 0.8460 (t0) REVERT: B 657 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8772 (mt-10) REVERT: C 69 TRP cc_start: 0.9274 (m-90) cc_final: 0.8801 (m-90) REVERT: C 113 ASP cc_start: 0.9084 (m-30) cc_final: 0.8837 (m-30) REVERT: C 424 MET cc_start: 0.7570 (tmm) cc_final: 0.7157 (tmm) REVERT: C 447 ILE cc_start: 0.9475 (OUTLIER) cc_final: 0.9252 (mp) REVERT: D 530 MET cc_start: 0.7152 (mtm) cc_final: 0.6928 (mtm) REVERT: D 601 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8354 (ptpp) REVERT: D 633 LYS cc_start: 0.9640 (mttm) cc_final: 0.9279 (mttp) REVERT: D 651 ASN cc_start: 0.8441 (t0) cc_final: 0.8195 (t0) REVERT: D 654 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7926 (tm-30) REVERT: D 657 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8712 (mt-10) REVERT: E 69 TRP cc_start: 0.9142 (m-90) cc_final: 0.8733 (m-90) REVERT: F 530 MET cc_start: 0.7064 (mtm) cc_final: 0.6836 (mtm) REVERT: F 601 LYS cc_start: 0.8913 (mtmm) cc_final: 0.8615 (ptpp) REVERT: F 651 ASN cc_start: 0.9079 (t0) cc_final: 0.8786 (t0) REVERT: F 654 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8428 (tm-30) REVERT: F 657 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8793 (mt-10) outliers start: 59 outliers final: 52 residues processed: 173 average time/residue: 0.2621 time to fit residues: 68.4697 Evaluate side-chains 175 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 121 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 ARG Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 116 optimal weight: 1.9990 chunk 176 optimal weight: 40.0000 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14973 Z= 0.194 Angle : 0.748 11.465 20331 Z= 0.368 Chirality : 0.050 0.289 2490 Planarity : 0.003 0.062 2520 Dihedral : 8.447 57.383 3121 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.53 % Favored : 88.35 % Rotamer: Outliers : 3.44 % Allowed : 21.85 % Favored : 74.71 % 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: -2.57 (0.20), residues: 1734 helix: -0.22 (0.27), residues: 426 sheet: -1.33 (0.27), residues: 345 loop : -2.65 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 571 HIS 0.002 0.001 HIS D 564 PHE 0.027 0.001 PHE C 360 TYR 0.007 0.001 TYR E 217 ARG 0.024 0.001 ARG B 557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8676 (m-30) cc_final: 0.8419 (t0) REVERT: A 260 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8666 (pp) REVERT: B 530 MET cc_start: 0.7414 (mtm) cc_final: 0.7128 (pmm) REVERT: B 626 MET cc_start: 0.8488 (ttm) cc_final: 0.8268 (ttm) REVERT: B 651 ASN cc_start: 0.8839 (t0) cc_final: 0.8550 (t0) REVERT: B 657 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8803 (mt-10) REVERT: C 69 TRP cc_start: 0.9277 (m-90) cc_final: 0.8845 (m-90) REVERT: C 113 ASP cc_start: 0.9035 (m-30) cc_final: 0.8783 (m-30) REVERT: C 125 LEU cc_start: 0.9618 (tp) cc_final: 0.9181 (tt) REVERT: C 447 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9236 (mp) REVERT: D 530 MET cc_start: 0.6994 (mtm) cc_final: 0.6703 (mtm) REVERT: D 601 LYS cc_start: 0.8862 (mtpp) cc_final: 0.8326 (ptpp) REVERT: D 633 LYS cc_start: 0.9634 (mttm) cc_final: 0.9270 (mttp) REVERT: D 657 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8718 (mt-10) REVERT: E 69 TRP cc_start: 0.9133 (m-90) cc_final: 0.8765 (m-90) REVERT: E 125 LEU cc_start: 0.9640 (tp) cc_final: 0.9152 (tt) REVERT: F 530 MET cc_start: 0.6888 (mtm) cc_final: 0.6647 (mtm) REVERT: F 601 LYS cc_start: 0.8879 (mtmm) cc_final: 0.8613 (ptpp) REVERT: F 651 ASN cc_start: 0.9061 (t0) cc_final: 0.8842 (t0) REVERT: F 654 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8438 (tm-30) REVERT: F 657 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8799 (mt-10) outliers start: 53 outliers final: 45 residues processed: 174 average time/residue: 0.2714 time to fit residues: 70.8538 Evaluate side-chains 175 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 ARG Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 123 optimal weight: 0.0070 chunk 8 optimal weight: 0.8980 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.050364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.040184 restraints weight = 96504.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.041308 restraints weight = 59491.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.042074 restraints weight = 43603.916| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14973 Z= 0.256 Angle : 0.763 10.238 20331 Z= 0.377 Chirality : 0.049 0.284 2490 Planarity : 0.003 0.062 2520 Dihedral : 8.457 57.428 3121 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.92 % Favored : 86.91 % Rotamer: Outliers : 3.57 % Allowed : 21.85 % Favored : 74.58 % 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: -2.46 (0.20), residues: 1734 helix: -0.04 (0.28), residues: 408 sheet: -1.15 (0.28), residues: 312 loop : -2.61 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 571 HIS 0.003 0.001 HIS C 105 PHE 0.028 0.001 PHE C 360 TYR 0.012 0.001 TYR C 217 ARG 0.023 0.001 ARG B 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2679.49 seconds wall clock time: 51 minutes 15.81 seconds (3075.81 seconds total)