Starting phenix.real_space_refine on Sun Mar 17 11:38:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/03_2024/8szg_40915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/03_2024/8szg_40915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/03_2024/8szg_40915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/03_2024/8szg_40915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/03_2024/8szg_40915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/03_2024/8szg_40915_updated.pdb" } resolution = 3.6 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= 0.048 sd= 0.126 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 3 5.49 5 S 100 5.16 5 C 11359 2.51 5 N 2904 2.21 5 O 3196 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17571 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2404 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 142 Chain: "E" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 368 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 6520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6520 Classifications: {'peptide': 830} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 32, 'TRANS': 797} Chain breaks: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "B" Number of atoms: 6279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6279 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 31, 'TRANS': 764} Chain breaks: 3 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1640 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 130 Chain: "F" 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: "G" 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: "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: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 159 Unusual residues: {' CA': 3, 'NAG': 2, 'PCW': 1, 'PO4': 1, 'SPM': 2, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1208 "'] Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 117 Unusual residues: {'CLR': 1, 'NAG': 2, 'PO4': 1, 'SPM': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1405 "'] Classifications: {'peptide': 1, 'undetermined': 6, 'water': 1} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.53, per 1000 atoms: 0.60 Number of scatterers: 17571 At special positions: 0 Unit cell: (102.389, 108.463, 251.633, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 100 16.00 P 3 15.00 F 6 9.00 O 3196 8.00 N 2904 7.00 C 11359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1202 " - " ASN A 287 " " NAG A1203 " - " ASN A 468 " " NAG B1402 " - " ASN B 468 " " NAG B1403 " - " ASN B 488 " " NAG F 1 " - " ASN A 488 " " NAG G 1 " - " ASN A 541 " " NAG H 1 " - " ASN B 541 " Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 3.4 seconds 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 20 sheets defined 38.4% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'D' and resid 7 through 25 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 10 through 23 Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'A' and resid 65 through 82 removed outlier: 3.757A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.614A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.749A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.879A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.458A pdb=" N HIS A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.730A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.563A pdb=" N LYS A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.544A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 611 through 636 removed outlier: 3.862A pdb=" N LEU A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 650 through 667 removed outlier: 4.039A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 707 removed outlier: 5.064A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix Processing helix chain 'A' and resid 717 through 745 removed outlier: 3.606A pdb=" N LEU A 723 " --> pdb=" O TRP A 719 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 729 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 793 removed outlier: 3.854A pdb=" N ILE A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 820 removed outlier: 3.565A pdb=" N LEU A 812 " --> pdb=" O THR A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 832 through 862 removed outlier: 3.844A pdb=" N PHE A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 866 No H-bonds generated for 'chain 'A' and resid 864 through 866' Processing helix chain 'A' and resid 869 through 884 Processing helix chain 'B' and resid 65 through 83 removed outlier: 3.588A pdb=" N ARG B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 116 through 119 No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.699A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 249 through 261 Processing helix chain 'B' and resid 273 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 308 through 314 removed outlier: 4.949A pdb=" N HIS B 312 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 417 through 435 removed outlier: 3.824A pdb=" N TYR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 611 through 636 removed outlier: 4.226A pdb=" N ALA B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 648 through 668 removed outlier: 3.579A pdb=" N PHE B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 698 removed outlier: 3.954A pdb=" N ARG B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLN B 681 " --> pdb=" O CYS B 677 " (cutoff:3.500A) Proline residue: B 682 - end of helix removed outlier: 3.512A pdb=" N ILE B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 705 No H-bonds generated for 'chain 'B' and resid 702 through 705' Processing helix chain 'B' and resid 723 through 745 removed outlier: 3.774A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 793 removed outlier: 3.688A pdb=" N ALA B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 827 removed outlier: 3.753A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 833 through 861 removed outlier: 3.606A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 37 removed outlier: 3.755A pdb=" N ARG C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 61 removed outlier: 3.539A pdb=" N GLN C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 288 through 291 No H-bonds generated for 'chain 'C' and resid 288 through 291' Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 337 through 355 Processing sheet with id= A, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.853A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 80 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 72 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 73 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 111 through 114 removed outlier: 3.519A pdb=" N CYS D 114 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER D 122 " --> pdb=" O CYS D 114 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 148 through 151 removed outlier: 3.804A pdb=" N CYS D 148 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.655A pdb=" N LYS D 209 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 201 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 200 " --> pdb=" O SER D 191 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 189 " --> pdb=" O GLY D 202 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 250 through 254 removed outlier: 3.552A pdb=" N ARG D 251 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 253 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 231 " --> pdb=" O GLY D 244 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 273 through 278 removed outlier: 6.552A pdb=" N GLY D 288 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 276 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU D 286 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE D 278 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU D 284 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 318 through 320 removed outlier: 3.509A pdb=" N LYS D 337 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN D 340 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR D 47 " --> pdb=" O ASN D 340 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.493A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA A 140 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N LEU A 37 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 142 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.727A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A 294 " --> pdb=" O VAL A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.678A pdb=" N ILE A 491 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 509 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 468 through 470 removed outlier: 3.636A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 602 through 604 removed outlier: 3.954A pdb=" N ILE A 763 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.635A pdb=" N TYR B 95 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 140 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N LEU B 37 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL B 142 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.601A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'B' and resid 318 through 321 removed outlier: 3.668A pdb=" N TYR B 489 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 509 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 468 through 470 Processing sheet with id= Q, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= R, first strand: chain 'B' and resid 602 through 604 Processing sheet with id= S, first strand: chain 'C' and resid 39 through 44 removed outlier: 6.688A pdb=" N ILE C 200 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU C 42 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG C 202 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU C 44 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL C 204 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE C 190 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 225 through 231 removed outlier: 6.866A pdb=" N SER C 268 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE C 228 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE C 270 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL C 230 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE C 272 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id= T 619 hydrogen bonds defined for protein. 1821 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: 5.92 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2955 1.32 - 1.46: 5579 1.46 - 1.59: 9309 1.59 - 1.72: 6 1.72 - 1.86: 127 Bond restraints: 17976 Sorted by residual: bond pdb=" C31 PCW A1204 " pdb=" O2 PCW A1204 " ideal model delta sigma weight residual 1.333 1.487 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" CG1 ILE C 337 " pdb=" CD1 ILE C 337 " ideal model delta sigma weight residual 1.513 1.267 0.246 3.90e-02 6.57e+02 3.96e+01 bond pdb=" C16 PCW A1204 " pdb=" C17 PCW A1204 " ideal model delta sigma weight residual 1.523 1.623 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C31 PCW A1204 " pdb=" C32 PCW A1204 " ideal model delta sigma weight residual 1.502 1.601 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C11 PCW A1204 " pdb=" O3 PCW A1204 " ideal model delta sigma weight residual 1.326 1.417 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 17971 not shown) Histogram of bond angle deviations from ideal: 88.88 - 101.62: 37 101.62 - 114.35: 10950 114.35 - 127.09: 13209 127.09 - 139.82: 204 139.82 - 152.56: 1 Bond angle restraints: 24401 Sorted by residual: angle pdb=" C PHE C 341 " pdb=" CA PHE C 341 " pdb=" CB PHE C 341 " ideal model delta sigma weight residual 110.85 88.88 21.97 1.70e+00 3.46e-01 1.67e+02 angle pdb=" C18 PCW A1204 " pdb=" C19 PCW A1204 " pdb=" C20 PCW A1204 " ideal model delta sigma weight residual 127.82 152.56 -24.74 3.00e+00 1.11e-01 6.80e+01 angle pdb=" C THR B 596 " pdb=" CA THR B 596 " pdb=" CB THR B 596 " ideal model delta sigma weight residual 110.88 98.18 12.70 1.57e+00 4.06e-01 6.54e+01 angle pdb=" N LYS C 345 " pdb=" CA LYS C 345 " pdb=" C LYS C 345 " ideal model delta sigma weight residual 111.07 103.21 7.86 1.07e+00 8.73e-01 5.40e+01 angle pdb=" N ILE B 434 " pdb=" CA ILE B 434 " pdb=" C ILE B 434 " ideal model delta sigma weight residual 110.72 103.40 7.32 1.01e+00 9.80e-01 5.25e+01 ... (remaining 24396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 10481 32.59 - 65.17: 266 65.17 - 97.76: 25 97.76 - 130.34: 1 130.34 - 162.93: 1 Dihedral angle restraints: 10774 sinusoidal: 4269 harmonic: 6505 Sorted by residual: dihedral pdb=" C PHE C 341 " pdb=" N PHE C 341 " pdb=" CA PHE C 341 " pdb=" CB PHE C 341 " ideal model delta harmonic sigma weight residual -122.60 -95.83 -26.77 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual -86.00 -176.09 90.09 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS B 585 " pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " pdb=" CB CYS B 598 " ideal model delta sinusoidal sigma weight residual -86.00 -169.45 83.45 1 1.00e+01 1.00e-02 8.50e+01 ... (remaining 10771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.027: 2785 1.027 - 2.053: 0 2.053 - 3.080: 0 3.080 - 4.107: 0 4.107 - 5.133: 1 Chirality restraints: 2786 Sorted by residual: chirality pdb=" C2 PCW A1204 " pdb=" C1 PCW A1204 " pdb=" C3 PCW A1204 " pdb=" O2 PCW A1204 " both_signs ideal model delta sigma weight residual False -2.32 2.81 -5.13 2.00e-01 2.50e+01 6.59e+02 chirality pdb=" CA ASP C 346 " pdb=" N ASP C 346 " pdb=" C ASP C 346 " pdb=" CB ASP C 346 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.48e+01 ... (remaining 2783 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 821 " -0.044 2.00e-02 2.50e+03 4.41e-02 3.40e+01 pdb=" CG PHE B 821 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE B 821 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 PHE B 821 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE B 821 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE B 821 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 821 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 792 " 0.030 2.00e-02 2.50e+03 3.97e-02 2.75e+01 pdb=" CG PHE B 792 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 792 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 PHE B 792 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE B 792 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 PHE B 792 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 792 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 712 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C THR A 712 " -0.073 2.00e-02 2.50e+03 pdb=" O THR A 712 " 0.028 2.00e-02 2.50e+03 pdb=" N SER A 713 " 0.024 2.00e-02 2.50e+03 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4774 2.80 - 3.33: 15683 3.33 - 3.85: 26863 3.85 - 4.38: 30588 4.38 - 4.90: 53705 Nonbonded interactions: 131613 Sorted by model distance: nonbonded pdb=" OG1 THR B 550 " pdb=" O VAL B 566 " model vdw 2.281 2.440 nonbonded pdb=" O SER D 31 " pdb=" OG SER D 31 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR D 102 " pdb=" O SER D 147 " model vdw 2.308 2.440 nonbonded pdb=" OE1 GLU B 229 " pdb=" NH1 ARG B 233 " model vdw 2.308 2.520 nonbonded pdb=" NH2 ARG B 69 " pdb=" O2 PO4 B1406 " model vdw 2.326 2.520 ... (remaining 131608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 118 or (resid 119 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 362 or resid 392 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 through 516 or (resid 517 and (name N or name CA or name C or name \ O or name CB )) or resid 518 through 546 or (resid 547 through 548 and (name N \ or name CA or name C or name O or name CB )) or resid 549 through 586 or (resid \ 587 through 588 and (name N or name CA or name C or name O or name CB )) or resi \ d 589 through 673 or (resid 674 and (name N or name CA or name C or name O or na \ me CB )) or resid 675 through 707 or resid 722 through 734 or (resid 735 and (na \ me N or name CA or name C or name O or name CB )) or resid 736 through 756 or (r \ esid 757 and (name N or name CA or name C or name O or name CB )) or resid 758 t \ hrough 801 or (resid 802 and (name N or name CA or name C or name O or name CB ) \ ) or resid 803 through 868 or (resid 869 through 871 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1208 through 1209)) selection = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 120 or (resid 134 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 through 360 or \ (resid 361 through 362 and (name N or name CA or name C or name O or name CB )) \ or resid 392 through 480 or (resid 481 and (name N or name CA or name C or name \ O or name CB )) or resid 482 through 498 or (resid 499 through 500 and (name N \ or name CA or name C or name O or name CB )) or resid 501 through 591 or (resid \ 592 through 593 and (name N or name CA or name C or name O or name CB )) or resi \ d 594 through 608 or (resid 609 through 610 and (name N or name CA or name C or \ name O or name CB )) or resid 611 through 670 or (resid 671 and (name N or name \ CA or name C or name O or name CB )) or resid 672 through 706 or (resid 707 thro \ ugh 722 and (name N or name CA or name C or name O or name CB )) or resid 723 th \ rough 871 or resid 1405 through 1406)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 7.320 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: 0.020 Extract box with map and model: 26.990 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 49.970 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 88.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.006 0.246 17976 Z= 0.418 Angle : 0.851 24.740 24401 Z= 0.519 Chirality : 0.114 5.133 2786 Planarity : 0.005 0.050 3061 Dihedral : 14.080 162.926 6504 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2209 helix: 0.79 (0.18), residues: 869 sheet: -0.76 (0.29), residues: 347 loop : -1.25 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 742 HIS 0.010 0.001 HIS A 879 PHE 0.085 0.003 PHE B 821 TYR 0.031 0.002 TYR B 829 ARG 0.018 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 301 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8753 (mppt) cc_final: 0.8405 (mmtm) REVERT: D 63 TRP cc_start: 0.7781 (m100) cc_final: 0.7371 (m100) REVERT: A 790 PHE cc_start: 0.8329 (m-10) cc_final: 0.7984 (m-80) REVERT: A 832 PHE cc_start: 0.6995 (m-10) cc_final: 0.6712 (m-80) REVERT: B 510 TYR cc_start: 0.8072 (p90) cc_final: 0.7869 (p90) REVERT: B 558 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 618 LEU cc_start: 0.7929 (mt) cc_final: 0.7534 (pp) REVERT: B 738 ILE cc_start: 0.7575 (tp) cc_final: 0.7296 (tt) REVERT: C 29 LEU cc_start: 0.8964 (tp) cc_final: 0.8689 (tt) REVERT: C 44 LEU cc_start: 0.7931 (tp) cc_final: 0.7509 (tp) REVERT: C 259 ILE cc_start: 0.8241 (mm) cc_final: 0.7756 (tt) REVERT: C 282 LYS cc_start: 0.7408 (mtpt) cc_final: 0.7189 (mtpp) outliers start: 2 outliers final: 1 residues processed: 303 average time/residue: 0.3016 time to fit residues: 136.4379 Evaluate side-chains 240 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 ASN ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 471 ASN B 700 ASN B 800 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17976 Z= 0.188 Angle : 0.537 9.266 24401 Z= 0.280 Chirality : 0.043 0.284 2786 Planarity : 0.004 0.040 3061 Dihedral : 8.526 74.140 2762 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.57 % Allowed : 8.72 % Favored : 89.71 % 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: -0.21 (0.18), residues: 2209 helix: 1.37 (0.18), residues: 858 sheet: -0.71 (0.28), residues: 383 loop : -1.27 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 818 HIS 0.007 0.001 HIS B 359 PHE 0.019 0.001 PHE A 814 TYR 0.018 0.001 TYR D 111 ARG 0.004 0.000 ARG B 535 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 255 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8766 (mppt) cc_final: 0.8419 (mmtm) REVERT: D 63 TRP cc_start: 0.7741 (m100) cc_final: 0.7316 (m100) REVERT: A 760 ILE cc_start: 0.8592 (mt) cc_final: 0.8162 (mm) REVERT: A 789 PHE cc_start: 0.8530 (t80) cc_final: 0.8194 (t80) REVERT: A 790 PHE cc_start: 0.8072 (m-10) cc_final: 0.7731 (m-80) REVERT: A 829 TYR cc_start: 0.7849 (p90) cc_final: 0.7462 (p90) REVERT: A 832 PHE cc_start: 0.6978 (m-10) cc_final: 0.6666 (m-80) REVERT: B 446 ASN cc_start: 0.7712 (t0) cc_final: 0.7434 (t0) REVERT: B 558 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7674 (mm-30) REVERT: B 852 ILE cc_start: 0.8456 (mt) cc_final: 0.8219 (mm) REVERT: C 29 LEU cc_start: 0.8933 (tp) cc_final: 0.8675 (tt) REVERT: C 44 LEU cc_start: 0.7851 (tp) cc_final: 0.7641 (tp) REVERT: C 259 ILE cc_start: 0.8116 (mm) cc_final: 0.7450 (pt) REVERT: C 321 ASP cc_start: 0.6875 (t0) cc_final: 0.6646 (t0) outliers start: 28 outliers final: 15 residues processed: 266 average time/residue: 0.3070 time to fit residues: 122.3454 Evaluate side-chains 247 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 232 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 167 optimal weight: 0.0970 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 800 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17976 Z= 0.205 Angle : 0.512 9.439 24401 Z= 0.267 Chirality : 0.043 0.231 2786 Planarity : 0.003 0.041 3061 Dihedral : 7.953 78.343 2761 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.23 % Allowed : 11.12 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2209 helix: 1.46 (0.18), residues: 864 sheet: -0.71 (0.29), residues: 365 loop : -1.30 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 818 HIS 0.007 0.001 HIS B 359 PHE 0.015 0.001 PHE A 814 TYR 0.013 0.001 TYR A 858 ARG 0.003 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 242 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8780 (mppt) cc_final: 0.8494 (mmtm) REVERT: D 63 TRP cc_start: 0.7717 (m100) cc_final: 0.7331 (m100) REVERT: D 234 PHE cc_start: 0.5364 (t80) cc_final: 0.5013 (t80) REVERT: A 760 ILE cc_start: 0.8595 (mt) cc_final: 0.8237 (mm) REVERT: A 789 PHE cc_start: 0.8435 (t80) cc_final: 0.8101 (t80) REVERT: A 790 PHE cc_start: 0.8130 (m-10) cc_final: 0.7742 (m-80) REVERT: A 829 TYR cc_start: 0.7888 (p90) cc_final: 0.7520 (p90) REVERT: A 832 PHE cc_start: 0.7056 (m-10) cc_final: 0.6752 (m-80) REVERT: A 866 ARG cc_start: 0.7098 (mtt90) cc_final: 0.6860 (mtt90) REVERT: B 446 ASN cc_start: 0.7762 (t0) cc_final: 0.7388 (t0) REVERT: B 558 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7684 (mm-30) REVERT: B 738 ILE cc_start: 0.7445 (tp) cc_final: 0.7173 (tt) REVERT: C 29 LEU cc_start: 0.8925 (tp) cc_final: 0.8690 (tt) REVERT: C 44 LEU cc_start: 0.8070 (tp) cc_final: 0.7680 (tp) REVERT: C 215 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8255 (mmmt) REVERT: C 259 ILE cc_start: 0.8163 (mm) cc_final: 0.7544 (pt) REVERT: C 312 MET cc_start: 0.8390 (tpp) cc_final: 0.8136 (tpp) REVERT: C 321 ASP cc_start: 0.7021 (t0) cc_final: 0.6722 (t0) outliers start: 22 outliers final: 15 residues processed: 250 average time/residue: 0.3031 time to fit residues: 114.2864 Evaluate side-chains 248 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 233 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 2.9990 chunk 151 optimal weight: 0.1980 chunk 104 optimal weight: 0.0030 chunk 22 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17976 Z= 0.133 Angle : 0.471 10.118 24401 Z= 0.245 Chirality : 0.041 0.227 2786 Planarity : 0.003 0.040 3061 Dihedral : 7.408 75.176 2761 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.51 % Allowed : 12.07 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2209 helix: 1.62 (0.18), residues: 861 sheet: -0.71 (0.28), residues: 366 loop : -1.23 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 263 HIS 0.004 0.001 HIS B 359 PHE 0.021 0.001 PHE C 341 TYR 0.012 0.001 TYR B 751 ARG 0.005 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 246 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8775 (mppt) cc_final: 0.8486 (mmtm) REVERT: D 63 TRP cc_start: 0.7713 (m100) cc_final: 0.7302 (m100) REVERT: D 234 PHE cc_start: 0.5303 (t80) cc_final: 0.5027 (t80) REVERT: A 760 ILE cc_start: 0.8610 (mt) cc_final: 0.8269 (mm) REVERT: A 789 PHE cc_start: 0.8352 (t80) cc_final: 0.8108 (t80) REVERT: A 790 PHE cc_start: 0.8085 (m-10) cc_final: 0.7789 (m-10) REVERT: A 811 MET cc_start: 0.6521 (mmm) cc_final: 0.6304 (mmp) REVERT: A 829 TYR cc_start: 0.7858 (p90) cc_final: 0.7562 (p90) REVERT: A 832 PHE cc_start: 0.7103 (m-10) cc_final: 0.6772 (m-80) REVERT: B 446 ASN cc_start: 0.7757 (t0) cc_final: 0.7340 (t0) REVERT: B 525 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6907 (mt-10) REVERT: B 558 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 738 ILE cc_start: 0.7466 (tp) cc_final: 0.7239 (tp) REVERT: C 27 ARG cc_start: 0.8083 (ttm170) cc_final: 0.7546 (ttp-170) REVERT: C 29 LEU cc_start: 0.8922 (tp) cc_final: 0.8676 (tt) REVERT: C 44 LEU cc_start: 0.8034 (tp) cc_final: 0.7791 (tp) REVERT: C 215 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8261 (mmmt) REVERT: C 259 ILE cc_start: 0.8139 (mm) cc_final: 0.7467 (pt) REVERT: C 312 MET cc_start: 0.8382 (tpp) cc_final: 0.8141 (tpp) REVERT: C 321 ASP cc_start: 0.7004 (t0) cc_final: 0.6785 (t0) outliers start: 27 outliers final: 17 residues processed: 260 average time/residue: 0.2896 time to fit residues: 114.2928 Evaluate side-chains 251 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 234 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17976 Z= 0.286 Angle : 0.541 10.194 24401 Z= 0.283 Chirality : 0.044 0.235 2786 Planarity : 0.004 0.041 3061 Dihedral : 7.449 75.991 2761 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.18 % Allowed : 12.74 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2209 helix: 1.46 (0.18), residues: 855 sheet: -0.79 (0.28), residues: 365 loop : -1.32 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 530 HIS 0.005 0.001 HIS A 429 PHE 0.023 0.001 PHE C 341 TYR 0.016 0.002 TYR E 40 ARG 0.004 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 235 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8802 (mppt) cc_final: 0.8513 (mmtm) REVERT: D 63 TRP cc_start: 0.7741 (m100) cc_final: 0.7286 (m100) REVERT: D 234 PHE cc_start: 0.5401 (t80) cc_final: 0.5164 (t80) REVERT: A 760 ILE cc_start: 0.8603 (mt) cc_final: 0.8249 (mm) REVERT: A 829 TYR cc_start: 0.7914 (p90) cc_final: 0.7642 (p90) REVERT: A 832 PHE cc_start: 0.7212 (m-10) cc_final: 0.6781 (m-80) REVERT: B 74 MET cc_start: 0.7713 (ttt) cc_final: 0.7488 (ttt) REVERT: B 446 ASN cc_start: 0.7799 (t0) cc_final: 0.7360 (t0) REVERT: B 558 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7748 (mm-30) REVERT: B 738 ILE cc_start: 0.7522 (tp) cc_final: 0.7251 (tt) REVERT: B 854 PHE cc_start: 0.7385 (m-80) cc_final: 0.7030 (m-80) REVERT: C 29 LEU cc_start: 0.8943 (tp) cc_final: 0.8696 (tt) REVERT: C 44 LEU cc_start: 0.8071 (tp) cc_final: 0.7829 (tp) REVERT: C 215 LYS cc_start: 0.8501 (mmmt) cc_final: 0.7303 (mmmt) REVERT: C 259 ILE cc_start: 0.8159 (mm) cc_final: 0.7503 (pt) REVERT: C 312 MET cc_start: 0.8393 (tpp) cc_final: 0.8127 (tpp) outliers start: 39 outliers final: 30 residues processed: 253 average time/residue: 0.2943 time to fit residues: 112.9667 Evaluate side-chains 252 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 17 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 471 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17976 Z= 0.175 Angle : 0.491 10.264 24401 Z= 0.257 Chirality : 0.042 0.229 2786 Planarity : 0.003 0.041 3061 Dihedral : 7.163 74.623 2761 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.01 % Allowed : 14.03 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2209 helix: 1.53 (0.18), residues: 862 sheet: -0.79 (0.28), residues: 379 loop : -1.32 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 263 HIS 0.004 0.001 HIS B 359 PHE 0.023 0.001 PHE C 341 TYR 0.014 0.001 TYR A 858 ARG 0.005 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8795 (mppt) cc_final: 0.8521 (mmtm) REVERT: D 63 TRP cc_start: 0.7741 (m100) cc_final: 0.7315 (m100) REVERT: A 760 ILE cc_start: 0.8593 (mt) cc_final: 0.8268 (mm) REVERT: A 829 TYR cc_start: 0.7884 (p90) cc_final: 0.7654 (p90) REVERT: A 832 PHE cc_start: 0.7141 (m-10) cc_final: 0.6760 (m-80) REVERT: B 446 ASN cc_start: 0.7833 (t0) cc_final: 0.7380 (t0) REVERT: B 558 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7693 (mm-30) REVERT: B 811 MET cc_start: 0.6562 (mmp) cc_final: 0.6324 (mmt) REVERT: B 854 PHE cc_start: 0.7420 (m-80) cc_final: 0.7081 (m-80) REVERT: C 29 LEU cc_start: 0.8940 (tp) cc_final: 0.8686 (tt) REVERT: C 44 LEU cc_start: 0.8038 (tp) cc_final: 0.7824 (tp) REVERT: C 215 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7807 (mmmt) REVERT: C 259 ILE cc_start: 0.8106 (mm) cc_final: 0.7433 (pt) outliers start: 36 outliers final: 28 residues processed: 247 average time/residue: 0.2811 time to fit residues: 107.2918 Evaluate side-chains 251 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 223 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17976 Z= 0.193 Angle : 0.494 10.223 24401 Z= 0.258 Chirality : 0.042 0.233 2786 Planarity : 0.003 0.040 3061 Dihedral : 6.984 73.085 2761 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.07 % Allowed : 14.81 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2209 helix: 1.55 (0.18), residues: 862 sheet: -0.78 (0.28), residues: 365 loop : -1.30 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 530 HIS 0.004 0.001 HIS B 359 PHE 0.038 0.001 PHE A 821 TYR 0.013 0.001 TYR B 751 ARG 0.005 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 230 time to evaluate : 2.015 Fit side-chains revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8797 (mppt) cc_final: 0.8521 (mmtm) REVERT: D 63 TRP cc_start: 0.7750 (m100) cc_final: 0.7315 (m100) REVERT: A 760 ILE cc_start: 0.8605 (mt) cc_final: 0.8269 (mm) REVERT: A 829 TYR cc_start: 0.7897 (p90) cc_final: 0.7661 (p90) REVERT: A 832 PHE cc_start: 0.7041 (m-10) cc_final: 0.6566 (m-80) REVERT: B 446 ASN cc_start: 0.7849 (t0) cc_final: 0.7390 (t0) REVERT: B 558 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 811 MET cc_start: 0.6582 (mmp) cc_final: 0.6381 (mmt) REVERT: B 854 PHE cc_start: 0.7423 (m-80) cc_final: 0.7123 (m-80) REVERT: C 29 LEU cc_start: 0.8951 (tp) cc_final: 0.8699 (tt) REVERT: C 44 LEU cc_start: 0.8031 (tp) cc_final: 0.7806 (tp) REVERT: C 215 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7730 (mmmt) REVERT: C 259 ILE cc_start: 0.8098 (mm) cc_final: 0.7455 (pt) REVERT: C 312 MET cc_start: 0.8325 (tpp) cc_final: 0.7912 (tmm) REVERT: C 321 ASP cc_start: 0.7057 (t0) cc_final: 0.6731 (t0) outliers start: 37 outliers final: 27 residues processed: 252 average time/residue: 0.2863 time to fit residues: 111.4173 Evaluate side-chains 250 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 223 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 41 optimal weight: 0.4980 chunk 135 optimal weight: 0.0970 chunk 145 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17976 Z= 0.134 Angle : 0.473 10.505 24401 Z= 0.244 Chirality : 0.041 0.231 2786 Planarity : 0.003 0.041 3061 Dihedral : 6.690 70.635 2761 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.34 % Allowed : 15.82 % Favored : 82.84 % 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: -0.01 (0.18), residues: 2209 helix: 1.71 (0.18), residues: 858 sheet: -0.78 (0.28), residues: 371 loop : -1.25 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 263 HIS 0.004 0.001 HIS A 359 PHE 0.033 0.001 PHE B 789 TYR 0.013 0.001 TYR B 751 ARG 0.004 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 225 time to evaluate : 2.048 Fit side-chains revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8790 (mppt) cc_final: 0.8513 (mmtm) REVERT: D 63 TRP cc_start: 0.7742 (m100) cc_final: 0.7327 (m100) REVERT: D 139 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6746 (mt) REVERT: A 719 TRP cc_start: 0.6999 (t60) cc_final: 0.6399 (t-100) REVERT: A 760 ILE cc_start: 0.8611 (mt) cc_final: 0.8276 (mm) REVERT: A 829 TYR cc_start: 0.7862 (p90) cc_final: 0.7628 (p90) REVERT: A 832 PHE cc_start: 0.7069 (m-10) cc_final: 0.6627 (m-80) REVERT: B 446 ASN cc_start: 0.7862 (t0) cc_final: 0.7402 (t0) REVERT: B 525 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6885 (mt-10) REVERT: B 558 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7703 (mm-30) REVERT: B 733 PHE cc_start: 0.7205 (t80) cc_final: 0.6947 (t80) REVERT: B 811 MET cc_start: 0.6542 (mmp) cc_final: 0.6260 (mmt) REVERT: B 854 PHE cc_start: 0.7430 (m-80) cc_final: 0.7141 (m-80) REVERT: C 44 LEU cc_start: 0.8017 (tp) cc_final: 0.7809 (tp) REVERT: C 215 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7747 (mmmt) REVERT: C 259 ILE cc_start: 0.8088 (mm) cc_final: 0.7447 (pt) REVERT: C 312 MET cc_start: 0.8239 (tpp) cc_final: 0.7901 (tmm) REVERT: C 321 ASP cc_start: 0.7073 (t0) cc_final: 0.6828 (t0) outliers start: 24 outliers final: 15 residues processed: 235 average time/residue: 0.2975 time to fit residues: 107.2520 Evaluate side-chains 237 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 221 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 0.0970 chunk 186 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 155 optimal weight: 0.0270 chunk 60 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17976 Z= 0.136 Angle : 0.481 10.813 24401 Z= 0.246 Chirality : 0.041 0.232 2786 Planarity : 0.003 0.041 3061 Dihedral : 6.378 68.227 2761 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.57 % Allowed : 15.93 % Favored : 82.50 % 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: 0.06 (0.18), residues: 2209 helix: 1.76 (0.18), residues: 856 sheet: -0.79 (0.28), residues: 366 loop : -1.18 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 169 HIS 0.004 0.001 HIS B 359 PHE 0.027 0.001 PHE B 789 TYR 0.013 0.001 TYR B 751 ARG 0.004 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 229 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8781 (mppt) cc_final: 0.8520 (mmtm) REVERT: D 63 TRP cc_start: 0.7739 (m100) cc_final: 0.7335 (m100) REVERT: D 139 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6738 (mt) REVERT: A 719 TRP cc_start: 0.6899 (t60) cc_final: 0.6332 (t-100) REVERT: A 760 ILE cc_start: 0.8574 (mt) cc_final: 0.8236 (mm) REVERT: A 829 TYR cc_start: 0.7876 (p90) cc_final: 0.7660 (p90) REVERT: A 832 PHE cc_start: 0.7055 (m-10) cc_final: 0.6633 (m-80) REVERT: B 446 ASN cc_start: 0.7872 (t0) cc_final: 0.7410 (t0) REVERT: B 525 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6864 (mt-10) REVERT: B 558 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 733 PHE cc_start: 0.7162 (t80) cc_final: 0.6887 (t80) REVERT: B 811 MET cc_start: 0.6552 (mmp) cc_final: 0.6324 (mmt) REVERT: B 854 PHE cc_start: 0.7409 (m-80) cc_final: 0.7170 (m-80) REVERT: C 44 LEU cc_start: 0.8016 (tp) cc_final: 0.7791 (tp) REVERT: C 259 ILE cc_start: 0.8081 (mm) cc_final: 0.7433 (pt) REVERT: C 321 ASP cc_start: 0.7046 (t0) cc_final: 0.6819 (t0) outliers start: 28 outliers final: 22 residues processed: 242 average time/residue: 0.3012 time to fit residues: 110.7444 Evaluate side-chains 248 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 225 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 99 optimal weight: 0.0570 chunk 145 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17976 Z= 0.224 Angle : 0.527 11.154 24401 Z= 0.273 Chirality : 0.043 0.270 2786 Planarity : 0.003 0.040 3061 Dihedral : 6.450 68.508 2761 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.62 % Allowed : 15.65 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2209 helix: 1.60 (0.18), residues: 861 sheet: -0.79 (0.28), residues: 360 loop : -1.25 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 339 HIS 0.004 0.001 HIS A 429 PHE 0.033 0.001 PHE A 821 TYR 0.015 0.001 TYR E 40 ARG 0.004 0.000 ARG A 866 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 223 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8779 (mppt) cc_final: 0.8515 (mmtm) REVERT: D 63 TRP cc_start: 0.7759 (m100) cc_final: 0.7328 (m100) REVERT: D 139 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6751 (mt) REVERT: A 760 ILE cc_start: 0.8584 (mt) cc_final: 0.8234 (mm) REVERT: A 821 PHE cc_start: 0.6576 (m-80) cc_final: 0.6200 (m-10) REVERT: B 74 MET cc_start: 0.7750 (ttt) cc_final: 0.7540 (ttt) REVERT: B 446 ASN cc_start: 0.7877 (t0) cc_final: 0.7422 (t0) REVERT: B 558 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 733 PHE cc_start: 0.7208 (t80) cc_final: 0.6928 (t80) REVERT: B 854 PHE cc_start: 0.7485 (m-80) cc_final: 0.7193 (m-80) REVERT: C 44 LEU cc_start: 0.8046 (tp) cc_final: 0.7823 (tp) REVERT: C 259 ILE cc_start: 0.8098 (mm) cc_final: 0.7462 (pt) REVERT: C 321 ASP cc_start: 0.7091 (t0) cc_final: 0.6868 (t0) outliers start: 29 outliers final: 24 residues processed: 239 average time/residue: 0.2913 time to fit residues: 106.8154 Evaluate side-chains 248 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 223 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 25 optimal weight: 0.0020 chunk 48 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 154 optimal weight: 0.0570 overall best weight: 0.7508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.087517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071283 restraints weight = 49934.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071201 restraints weight = 44226.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071810 restraints weight = 40344.419| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17976 Z= 0.174 Angle : 0.510 13.230 24401 Z= 0.263 Chirality : 0.042 0.262 2786 Planarity : 0.003 0.040 3061 Dihedral : 6.291 67.396 2761 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.57 % Allowed : 15.99 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 2209 helix: 1.66 (0.18), residues: 860 sheet: -0.80 (0.28), residues: 356 loop : -1.24 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 530 HIS 0.004 0.001 HIS B 359 PHE 0.024 0.001 PHE A 821 TYR 0.014 0.001 TYR E 40 ARG 0.003 0.000 ARG A 866 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.60 seconds wall clock time: 64 minutes 12.29 seconds (3852.29 seconds total)