Starting phenix.real_space_refine on Mon Apr 8 13:18:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tao_41139/04_2024/8tao_41139_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tao_41139/04_2024/8tao_41139.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tao_41139/04_2024/8tao_41139_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tao_41139/04_2024/8tao_41139_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tao_41139/04_2024/8tao_41139_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tao_41139/04_2024/8tao_41139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tao_41139/04_2024/8tao_41139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tao_41139/04_2024/8tao_41139_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tao_41139/04_2024/8tao_41139_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 150 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 8509 2.51 5 N 2286 2.21 5 O 2514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13422 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 5804 Classifications: {'peptide': 777} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 744} Chain breaks: 2 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 415 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 171 Chain: "B" Number of atoms: 5694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5694 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 738} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 408 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 9, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 228 Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 939 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 931 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'QUS': 1, 'YKU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.28, per 1000 atoms: 0.54 Number of scatterers: 13422 At special positions: 0 Unit cell: (109.989, 85.547, 208.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 2514 8.00 N 2286 7.00 C 8509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 2.4 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3326 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 23 sheets defined 39.2% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 102 through 120 removed outlier: 4.491A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 removed outlier: 3.707A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 180 removed outlier: 3.829A pdb=" N SER A 180 " --> pdb=" O MET A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 180' Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 222 through 238 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.980A pdb=" N HIS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 335 through 343 removed outlier: 4.413A pdb=" N LYS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 418 removed outlier: 3.907A pdb=" N MET A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.753A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 604 removed outlier: 3.585A pdb=" N ALA A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 615 through 635 Processing helix chain 'A' and resid 641 through 671 removed outlier: 3.718A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 649 " --> pdb=" O TYR A 645 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 654 " --> pdb=" O GLY A 650 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.717A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 714 removed outlier: 3.651A pdb=" N VAL A 695 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 760 Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 775 through 794 Proline residue: A 790 - end of helix removed outlier: 4.312A pdb=" N PHE A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 794 " --> pdb=" O PRO A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 825 Proline residue: A 820 - end of helix Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 102 through 119 removed outlier: 4.635A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 removed outlier: 4.272A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 180 removed outlier: 3.521A pdb=" N SER B 180 " --> pdb=" O MET B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 180' Processing helix chain 'B' and resid 195 through 208 Processing helix chain 'B' and resid 222 through 237 removed outlier: 4.265A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.666A pdb=" N LYS B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 261 " --> pdb=" O PHE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 335 through 343 removed outlier: 3.603A pdb=" N ASP B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.921A pdb=" N GLN B 360 " --> pdb=" O GLN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 418 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.896A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 603 removed outlier: 3.735A pdb=" N ALA B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 590 " --> pdb=" O PHE B 586 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 601 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 612 Processing helix chain 'B' and resid 615 through 636 removed outlier: 3.937A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 672 removed outlier: 3.868A pdb=" N GLY B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 3.523A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 714 removed outlier: 3.536A pdb=" N ILE B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 761 Proline residue: B 743 - end of helix removed outlier: 3.634A pdb=" N ASN B 747 " --> pdb=" O PRO B 743 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 748 " --> pdb=" O LEU B 744 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 749 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 750 " --> pdb=" O TYR B 746 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 759 " --> pdb=" O THR B 755 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 794 Proline residue: B 790 - end of helix removed outlier: 3.553A pdb=" N PHE B 793 " --> pdb=" O VAL B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 816 Processing helix chain 'B' and resid 819 through 825 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.130A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'A' and resid 245 through 248 removed outlier: 6.906A pdb=" N ALA A 216 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ILE A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS A 218 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR A 219 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 300 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N CYS A 276 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU A 302 " --> pdb=" O CYS A 276 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 325 through 329 removed outlier: 6.440A pdb=" N ASN A 470 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASN A 483 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS A 472 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR A 481 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 445 through 447 Processing sheet with id= F, first strand: chain 'A' and resid 520 through 523 Processing sheet with id= G, first strand: chain 'A' and resid 556 through 558 Processing sheet with id= H, first strand: chain 'A' and resid 719 through 722 Processing sheet with id= I, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.296A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= K, first strand: chain 'B' and resid 245 through 248 removed outlier: 6.957A pdb=" N ALA B 216 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ILE B 248 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS B 218 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 300 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N CYS B 276 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 302 " --> pdb=" O CYS B 276 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.530A pdb=" N TRP B 487 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN B 470 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN B 483 " --> pdb=" O ASN B 470 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS B 472 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR B 481 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 445 through 447 Processing sheet with id= N, first strand: chain 'B' and resid 520 through 523 Processing sheet with id= O, first strand: chain 'B' and resid 541 through 543 Processing sheet with id= P, first strand: chain 'B' and resid 719 through 722 Processing sheet with id= Q, first strand: chain 'C' and resid 6 through 9 Processing sheet with id= R, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.450A pdb=" N THR C 122 " --> pdb=" O VAL C 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.711A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG C 40 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N SER C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 99 through 101 removed outlier: 3.746A pdb=" N TYR C 114 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 5 through 9 Processing sheet with id= V, first strand: chain 'D' and resid 12 through 15 removed outlier: 3.837A pdb=" N ALA D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG D 40 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N SER D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.592A pdb=" N TYR D 114 " --> pdb=" O ALA D 100 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1632 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: 4.71 Time building geometry restraints manager: 5.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2207 1.27 - 1.41: 3455 1.41 - 1.54: 7861 1.54 - 1.68: 35 1.68 - 1.82: 163 Bond restraints: 13721 Sorted by residual: bond pdb=" C04 QUS B 902 " pdb=" N14 QUS B 902 " ideal model delta sigma weight residual 1.324 1.439 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C04 QUS A 901 " pdb=" N14 QUS A 901 " ideal model delta sigma weight residual 1.324 1.438 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C05 QUS A 901 " pdb=" N15 QUS A 901 " ideal model delta sigma weight residual 1.331 1.440 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C05 QUS B 902 " pdb=" N15 QUS B 902 " ideal model delta sigma weight residual 1.331 1.440 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C05 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 13716 not shown) Histogram of bond angle deviations from ideal: 99.91 - 115.92: 8884 115.92 - 131.93: 9735 131.93 - 147.94: 34 147.94 - 163.95: 0 163.95 - 179.96: 1 Bond angle restraints: 18654 Sorted by residual: angle pdb=" C10 YKU B 901 " pdb=" N09 YKU B 901 " pdb=" C23 YKU B 901 " ideal model delta sigma weight residual 141.24 127.19 14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" C23 YKU B 901 " pdb=" N09 YKU B 901 " pdb=" N08 YKU B 901 " ideal model delta sigma weight residual 110.12 122.83 -12.71 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CA LEU B 567 " pdb=" CB LEU B 567 " pdb=" CG LEU B 567 " ideal model delta sigma weight residual 116.30 126.22 -9.92 3.50e+00 8.16e-02 8.04e+00 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N ASN A 222 " ideal model delta sigma weight residual 114.23 116.54 -2.31 8.80e-01 1.29e+00 6.91e+00 angle pdb=" N GLY A 65 " pdb=" CA GLY A 65 " pdb=" C GLY A 65 " ideal model delta sigma weight residual 113.18 118.71 -5.53 2.37e+00 1.78e-01 5.45e+00 ... (remaining 18649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 7392 17.69 - 35.38: 612 35.38 - 53.06: 123 53.06 - 70.75: 14 70.75 - 88.44: 8 Dihedral angle restraints: 8149 sinusoidal: 2958 harmonic: 5191 Sorted by residual: dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 549 " pdb=" CB CYS B 549 " ideal model delta sinusoidal sigma weight residual 93.00 162.29 -69.29 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS B 515 " pdb=" SG CYS B 515 " pdb=" SG CYS B 534 " pdb=" CB CYS B 534 " ideal model delta sinusoidal sigma weight residual -86.00 -140.14 54.14 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" CB CYS A 515 " pdb=" SG CYS A 515 " pdb=" SG CYS A 534 " pdb=" CB CYS A 534 " ideal model delta sinusoidal sigma weight residual -86.00 -123.82 37.82 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 8146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1370 0.034 - 0.069: 528 0.069 - 0.103: 131 0.103 - 0.137: 59 0.137 - 0.172: 3 Chirality restraints: 2091 Sorted by residual: chirality pdb=" CA ILE A 520 " pdb=" N ILE A 520 " pdb=" C ILE A 520 " pdb=" CB ILE A 520 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA ILE A 774 " pdb=" N ILE A 774 " pdb=" C ILE A 774 " pdb=" CB ILE A 774 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA VAL A 819 " pdb=" N VAL A 819 " pdb=" C VAL A 819 " pdb=" CB VAL A 819 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2088 not shown) Planarity restraints: 2393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 89 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO C 90 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 410 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C GLY A 410 " -0.023 2.00e-02 2.50e+03 pdb=" O GLY A 410 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 411 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 107 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO C 108 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 108 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 108 " -0.015 5.00e-02 4.00e+02 ... (remaining 2390 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2273 2.76 - 3.30: 12652 3.30 - 3.83: 21509 3.83 - 4.37: 24920 4.37 - 4.90: 43993 Nonbonded interactions: 105347 Sorted by model distance: nonbonded pdb=" OH TYR A 209 " pdb=" OD1 ASP A 496 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR B 311 " pdb=" OD1 ASP B 480 " model vdw 2.263 2.440 nonbonded pdb=" O LEU A 591 " pdb=" OG1 THR A 594 " model vdw 2.265 2.440 nonbonded pdb=" OG SER C 54 " pdb=" O GLY C 57 " model vdw 2.280 2.440 nonbonded pdb=" O GLY B 624 " pdb=" OG SER B 654 " model vdw 2.280 2.440 ... (remaining 105342 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 25 through 297 or (resid 298 and (name N or name CA or nam \ e C or name O or name CB )) or resid 299 through 378 or (resid 379 and (name N o \ r name CA or name C or name O or name CB )) or resid 380 through 523 or (resid 5 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 525 through \ 595 or (resid 596 and (name N or name CA or name C or name O or name CB )) or r \ esid 597 through 602 or (resid 603 and (name N or name CA or name C or name O or \ name CB )) or resid 604 through 619 or (resid 620 and (name N or name CA or nam \ e C or name O or name CB )) or resid 621 or (resid 622 through 623 and (name N o \ r name CA or name C or name O or name CB )) or (resid 624 through 627 and (name \ N or name CA or name C or name O or name CB )) or resid 628 through 632 or (resi \ d 633 and (name N or name CA or name C or name O or name CB )) or resid 634 thro \ ugh 638 or (resid 639 through 641 and (name N or name CA or name C or name O or \ name CB )) or resid 642 through 644 or (resid 645 through 646 and (name N or nam \ e CA or name C or name O or name CB )) or resid 647 through 662 or (resid 663 an \ d (name N or name CA or name C or name O or name CB )) or resid 664 or (resid 66 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 666 through \ 671 or (resid 672 through 673 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 688 or (resid 689 through 695 and (name N or name CA \ or name C or name O or name CB )) or resid 696 through 698 or (resid 699 throug \ h 700 and (name N or name CA or name C or name O or name CB )) or resid 701 thro \ ugh 707 or (resid 708 through 715 and (name N or name CA or name C or name O or \ name CB )) or resid 716 through 736 or (resid 737 through 738 and (name N or nam \ e CA or name C or name O or name CB )) or resid 739 through 741 or (resid 742 an \ d (name N or name CA or name C or name O or name CB )) or resid 743 through 750 \ or (resid 751 through 753 and (name N or name CA or name C or name O or name CB \ )) or resid 754 through 756 or (resid 757 through 760 and (name N or name CA or \ name C or name O or name CB )) or resid 761 through 768 or (resid 769 through 77 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 773 through \ 775 or (resid 776 and (name N or name CA or name C or name O or name CB )) or re \ sid 777 through 778 or (resid 779 and (name N or name CA or name C or name O or \ name CB )) or resid 780 through 782 or (resid 783 and (name N or name CA or name \ C or name O or name CB )) or resid 784 through 787 or (resid 788 and (name N or \ name CA or name C or name O or name CB )) or resid 789 through 795 or (resid 79 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 797 through \ 803 or (resid 804 and (name N or name CA or name C or name O or name CB )) or re \ sid 805 through 822 or (resid 823 through 826 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'B' and (resid 25 through 121 or (resid 140 and (name N or name CA or nam \ e C or name O or name CB )) or resid 141 through 559 or (resid 560 and (name N o \ r name CA or name C or name O or name CB )) or resid 561 through 566 or (resid 5 \ 67 and (name N or name CA or name C or name O or name CB )) or resid 568 through \ 580 or (resid 581 through 583 and (name N or name CA or name C or name O or nam \ e CB )) or resid 584 or (resid 585 and (name N or name CA or name C or name O or \ name CB )) or resid 586 through 587 or (resid 588 through 589 and (name N or na \ me CA or name C or name O or name CB )) or resid 590 through 600 or (resid 601 t \ hrough 603 and (name N or name CA or name C or name O or name CB )) or resid 604 \ through 617 or (resid 618 through 620 and (name N or name CA or name C or name \ O or name CB )) or resid 621 through 637 or (resid 638 through 641 and (name N o \ r name CA or name C or name O or name CB )) or resid 642 or (resid 643 and (name \ N or name CA or name C or name O or name CB )) or resid 644 through 650 or (res \ id 651 and (name N or name CA or name C or name O or name CB )) or resid 652 thr \ ough 653 or (resid 654 and (name N or name CA or name C or name O or name CB )) \ or resid 655 through 656 or (resid 657 through 658 and (name N or name CA or nam \ e C or name O or name CB )) or resid 659 or (resid 660 through 661 and (name N o \ r name CA or name C or name O or name CB )) or resid 662 through 666 or (resid 6 \ 67 through 673 and (name N or name CA or name C or name O or name CB )) or resid \ 687 or (resid 688 through 695 and (name N or name CA or name C or name O or nam \ e CB )) or resid 696 through 697 or (resid 698 through 700 and (name N or name C \ A or name C or name O or name CB )) or resid 701 or (resid 702 and (name N or na \ me CA or name C or name O or name CB )) or resid 703 through 721 or (resid 722 t \ hrough 723 and (name N or name CA or name C or name O or name CB )) or resid 724 \ through 743 or (resid 744 and (name N or name CA or name C or name O or name CB \ )) or resid 745 through 785 or (resid 786 through 788 and (name N or name CA or \ name C or name O or name CB )) or resid 789 through 820 or (resid 821 through 8 \ 26 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'C' and (resid 3 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 125)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 8.840 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 38.240 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.004 0.115 13721 Z= 0.246 Angle : 0.517 14.047 18654 Z= 0.264 Chirality : 0.041 0.172 2091 Planarity : 0.003 0.041 2393 Dihedral : 13.355 88.441 4763 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.43 (0.20), residues: 1778 helix: 1.81 (0.20), residues: 696 sheet: -0.35 (0.31), residues: 272 loop : -0.84 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 211 HIS 0.002 0.000 HIS B 267 PHE 0.013 0.001 PHE A 818 TYR 0.010 0.001 TYR A 223 ARG 0.005 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.529 Fit side-chains REVERT: A 524 ARG cc_start: 0.5996 (ttt180) cc_final: 0.5766 (ttt180) REVERT: A 547 TYR cc_start: 0.7161 (m-10) cc_final: 0.6935 (m-10) REVERT: B 229 GLU cc_start: 0.6041 (pt0) cc_final: 0.5757 (pt0) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 1.3678 time to fit residues: 215.3081 Evaluate side-chains 129 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13721 Z= 0.334 Angle : 0.563 9.198 18654 Z= 0.292 Chirality : 0.043 0.144 2091 Planarity : 0.004 0.040 2393 Dihedral : 4.777 83.672 1939 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.33 % Allowed : 7.41 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.40 (0.20), residues: 1778 helix: 1.90 (0.19), residues: 707 sheet: -0.45 (0.32), residues: 268 loop : -0.98 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.004 0.001 HIS A 218 PHE 0.016 0.001 PHE A 337 TYR 0.013 0.001 TYR A 409 ARG 0.004 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: A 255 GLN cc_start: 0.6706 (OUTLIER) cc_final: 0.6460 (mp10) REVERT: C 120 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8211 (tp-100) REVERT: D 5 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7625 (tt0) outliers start: 18 outliers final: 7 residues processed: 135 average time/residue: 1.3971 time to fit residues: 205.5188 Evaluate side-chains 138 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain D residue 5 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 110 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 174 optimal weight: 0.1980 chunk 144 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13721 Z= 0.239 Angle : 0.509 9.997 18654 Z= 0.264 Chirality : 0.041 0.132 2091 Planarity : 0.003 0.041 2393 Dihedral : 4.659 84.523 1939 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.26 % Allowed : 10.01 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.48 (0.20), residues: 1778 helix: 2.00 (0.19), residues: 706 sheet: -0.36 (0.32), residues: 268 loop : -0.98 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.003 0.001 HIS B 218 PHE 0.013 0.001 PHE B 358 TYR 0.009 0.001 TYR B 209 ARG 0.005 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.365 Fit side-chains REVERT: A 255 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.6331 (mp10) REVERT: D 5 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7626 (tt0) outliers start: 17 outliers final: 8 residues processed: 134 average time/residue: 1.3657 time to fit residues: 199.4698 Evaluate side-chains 139 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain D residue 5 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 108 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 0.0030 chunk 46 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN C 84 GLN D 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13721 Z= 0.147 Angle : 0.463 7.657 18654 Z= 0.241 Chirality : 0.040 0.127 2091 Planarity : 0.003 0.041 2393 Dihedral : 4.461 84.028 1939 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.41 % Allowed : 11.56 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.62 (0.20), residues: 1778 helix: 2.07 (0.19), residues: 708 sheet: -0.25 (0.32), residues: 268 loop : -0.88 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.001 0.000 HIS A 218 PHE 0.010 0.001 PHE B 358 TYR 0.007 0.001 TYR A 223 ARG 0.006 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.592 Fit side-chains REVERT: A 255 GLN cc_start: 0.6502 (OUTLIER) cc_final: 0.6264 (mp10) REVERT: C 120 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8131 (tp-100) REVERT: D 5 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7591 (tt0) outliers start: 19 outliers final: 7 residues processed: 136 average time/residue: 1.3644 time to fit residues: 203.2480 Evaluate side-chains 135 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain D residue 5 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 70 optimal weight: 30.0000 chunk 146 optimal weight: 20.0000 chunk 118 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 40.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN C 84 GLN D 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13721 Z= 0.397 Angle : 0.585 9.653 18654 Z= 0.301 Chirality : 0.044 0.152 2091 Planarity : 0.004 0.040 2393 Dihedral : 4.816 85.403 1939 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.78 % Allowed : 12.97 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.44 (0.20), residues: 1778 helix: 2.00 (0.20), residues: 708 sheet: -0.38 (0.31), residues: 267 loop : -1.06 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 211 HIS 0.005 0.001 HIS A 218 PHE 0.018 0.001 PHE A 337 TYR 0.012 0.001 TYR A 223 ARG 0.006 0.001 ARG C 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.560 Fit side-chains revert: symmetry clash REVERT: D 5 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7639 (tt0) outliers start: 24 outliers final: 10 residues processed: 136 average time/residue: 1.3027 time to fit residues: 194.3955 Evaluate side-chains 136 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain D residue 5 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 30.0000 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 90 optimal weight: 0.4980 chunk 166 optimal weight: 0.0270 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13721 Z= 0.151 Angle : 0.475 11.110 18654 Z= 0.245 Chirality : 0.040 0.131 2091 Planarity : 0.003 0.041 2393 Dihedral : 4.498 83.611 1939 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.26 % Allowed : 15.12 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.58 (0.20), residues: 1778 helix: 2.10 (0.20), residues: 711 sheet: -0.33 (0.32), residues: 257 loop : -0.96 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 211 HIS 0.002 0.000 HIS A 361 PHE 0.009 0.001 PHE B 358 TYR 0.008 0.001 TYR D 112 ARG 0.006 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.989 Fit side-chains revert: symmetry clash REVERT: B 40 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8410 (mt) REVERT: C 120 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8217 (tp-100) REVERT: D 5 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7605 (tt0) outliers start: 17 outliers final: 5 residues processed: 133 average time/residue: 1.3778 time to fit residues: 200.5068 Evaluate side-chains 134 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain D residue 5 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 chunk 97 optimal weight: 0.4980 chunk 144 optimal weight: 30.0000 chunk 96 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 107 optimal weight: 0.0170 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 106 optimal weight: 0.5980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13721 Z= 0.137 Angle : 0.472 12.622 18654 Z= 0.239 Chirality : 0.040 0.135 2091 Planarity : 0.003 0.040 2393 Dihedral : 4.333 83.734 1939 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.41 % Allowed : 15.27 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1778 helix: 2.19 (0.19), residues: 716 sheet: -0.20 (0.33), residues: 257 loop : -0.88 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.001 0.000 HIS A 361 PHE 0.008 0.001 PHE A 337 TYR 0.007 0.001 TYR D 112 ARG 0.007 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: C 120 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8144 (tp-100) REVERT: D 5 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7584 (tt0) outliers start: 19 outliers final: 8 residues processed: 134 average time/residue: 1.3380 time to fit residues: 197.2541 Evaluate side-chains 133 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain D residue 5 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 0.0770 chunk 15 optimal weight: 0.9980 chunk 134 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13721 Z= 0.161 Angle : 0.482 12.154 18654 Z= 0.242 Chirality : 0.040 0.133 2091 Planarity : 0.003 0.040 2393 Dihedral : 4.330 84.307 1939 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.11 % Allowed : 15.72 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.72 (0.21), residues: 1778 helix: 2.22 (0.19), residues: 716 sheet: -0.28 (0.32), residues: 267 loop : -0.90 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 211 HIS 0.002 0.000 HIS A 218 PHE 0.010 0.001 PHE A 337 TYR 0.007 0.001 TYR D 103 ARG 0.006 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: B 40 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8411 (mt) REVERT: C 120 GLN cc_start: 0.8513 (tp-100) cc_final: 0.8155 (tp-100) REVERT: D 5 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7585 (tt0) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 1.3733 time to fit residues: 191.8601 Evaluate side-chains 136 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain D residue 5 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 20.0000 chunk 159 optimal weight: 0.0980 chunk 164 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 151 optimal weight: 0.4980 chunk 104 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN B 157 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13721 Z= 0.146 Angle : 0.472 11.192 18654 Z= 0.239 Chirality : 0.040 0.139 2091 Planarity : 0.003 0.040 2393 Dihedral : 4.283 84.293 1939 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.11 % Allowed : 15.86 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.77 (0.21), residues: 1778 helix: 2.24 (0.19), residues: 716 sheet: -0.14 (0.33), residues: 257 loop : -0.89 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 211 HIS 0.001 0.000 HIS A 361 PHE 0.009 0.001 PHE A 337 TYR 0.007 0.001 TYR D 112 ARG 0.007 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: B 40 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8396 (mt) REVERT: C 120 GLN cc_start: 0.8509 (tp-100) cc_final: 0.8152 (tp-100) REVERT: D 5 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7563 (tt0) outliers start: 15 outliers final: 8 residues processed: 129 average time/residue: 1.3743 time to fit residues: 193.7001 Evaluate side-chains 135 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain D residue 5 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN B 157 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13721 Z= 0.234 Angle : 0.521 14.209 18654 Z= 0.261 Chirality : 0.041 0.133 2091 Planarity : 0.003 0.040 2393 Dihedral : 4.429 85.101 1939 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.26 % Allowed : 15.86 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.71 (0.21), residues: 1778 helix: 2.17 (0.19), residues: 721 sheet: -0.16 (0.32), residues: 268 loop : -0.93 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.002 0.001 HIS A 218 PHE 0.013 0.001 PHE A 337 TYR 0.008 0.001 TYR A 223 ARG 0.006 0.000 ARG A 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 330 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: B 40 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8512 (mt) REVERT: C 120 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8287 (tp-100) REVERT: D 5 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7596 (tt0) outliers start: 17 outliers final: 10 residues processed: 132 average time/residue: 1.4131 time to fit residues: 203.7862 Evaluate side-chains 137 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain D residue 5 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN B 157 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.133217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.091185 restraints weight = 26824.370| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.79 r_work: 0.3127 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13721 Z= 0.190 Angle : 0.504 13.474 18654 Z= 0.253 Chirality : 0.041 0.133 2091 Planarity : 0.003 0.041 2393 Dihedral : 4.393 84.753 1939 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.19 % Allowed : 15.94 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.70 (0.21), residues: 1778 helix: 2.21 (0.19), residues: 719 sheet: -0.28 (0.31), residues: 278 loop : -0.93 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.002 0.000 HIS A 361 PHE 0.011 0.001 PHE A 337 TYR 0.007 0.001 TYR A 223 ARG 0.007 0.000 ARG C 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4475.45 seconds wall clock time: 81 minutes 0.74 seconds (4860.74 seconds total)