Starting phenix.real_space_refine on Wed Apr 10 00:18:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/04_2024/8szi_40917_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/04_2024/8szi_40917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/04_2024/8szi_40917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/04_2024/8szi_40917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/04_2024/8szi_40917_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/04_2024/8szi_40917_updated.pdb" } resolution = 3.5 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= 0.020 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 C 11526 2.51 5 N 2932 2.21 5 O 3294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A GLU 757": "OE1" <-> "OE2" Residue "A GLU 759": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17868 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1765 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2509 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 80 Chain: "E" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 408 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 6538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 826, 6524 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 32, 'TRANS': 793} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 826, 6524 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 32, 'TRANS': 793} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 6676 Chain: "B" Number of atoms: 6327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6327 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 31, 'TRANS': 770} Chain breaks: 3 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 105 Unusual residues: {' CA': 2, 'NAG': 1, 'PCW': 1, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1005 "'] Classifications: {'peptide': 2, 'undetermined': 5} Modifications used: {'COO': 2} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 132 Unusual residues: {' CA': 2, 'CLR': 1, 'NAG': 2, 'PCW': 1, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1407 "'] Classifications: {'peptide': 1, 'undetermined': 7} 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 818 " occ=0.70 ... (26 atoms not shown) pdb=" CH2BTRP A 818 " occ=0.30 Time building chain proxies: 12.48, per 1000 atoms: 0.70 Number of scatterers: 17868 At special positions: 0 Unit cell: (99.7855, 118.007, 249.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 108 16.00 P 4 15.00 O 3294 8.00 N 2932 7.00 C 11526 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=2.04 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=2.04 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=2.04 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=2.06 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 A1002 " - " ASN A 468 " " NAG B1403 " - " ASN B 468 " " NAG B1404 " - " 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: 7.16 Conformation dependent library (CDL) restraints added in 4.3 seconds 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 22 sheets defined 38.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'C' and resid 8 through 32 removed outlier: 3.677A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 53 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.941A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 296 through 310 removed outlier: 4.051A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 4 through 24 Processing helix chain 'D' and resid 30 through 33 No H-bonds generated for 'chain 'D' and resid 30 through 33' 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 9 through 23 Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 45 through 47 No H-bonds generated for 'chain 'E' and resid 45 through 47' Processing helix chain 'A' and resid 65 through 82 removed outlier: 3.680A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.788A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 220 through 232 Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 273 through 285 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.540A pdb=" N PHE A 311 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.662A 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 416 through 435 removed outlier: 3.544A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 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: 4.282A pdb=" N ALA A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 648 through 668 removed outlier: 4.083A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N PHE A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 677 No H-bonds generated for 'chain 'A' and resid 674 through 677' Processing helix chain 'A' and resid 680 through 707 removed outlier: 4.418A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 702 " --> pdb=" O LYS A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 745 removed outlier: 4.012A pdb=" N PHE A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 796 removed outlier: 3.558A pdb=" N PHE A 788 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS A 796 " --> pdb=" O PHE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 827 removed outlier: 3.546A pdb=" N ILE A 822 " --> pdb=" O ATRP A 818 " (cutoff:3.500A) Proline residue: A 823 - end of helix Processing helix chain 'A' and resid 831 through 861 removed outlier: 4.920A pdb=" N PHE A 854 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN A 855 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 857 " --> pdb=" O PHE A 854 " (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 879 removed outlier: 4.230A pdb=" N HIS A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 removed outlier: 3.597A pdb=" N ARG B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP B 70 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 72 " --> pdb=" O PHE B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 removed outlier: 4.093A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.603A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.339A 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 204 Processing helix chain 'B' and resid 219 through 232 removed outlier: 3.719A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 259 removed outlier: 3.629A pdb=" N VAL B 258 " --> pdb=" O HIS B 254 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) 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: 5.078A pdb=" N HIS B 312 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.644A pdb=" N LYS B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) 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: 3.962A 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 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' 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 611 through 636 removed outlier: 3.681A pdb=" N ALA B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 648 through 667 removed outlier: 3.921A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU B 666 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 697 removed outlier: 4.749A pdb=" N GLN B 681 " --> pdb=" O CYS B 677 " (cutoff:3.500A) Proline residue: B 682 - end of helix Processing helix chain 'B' and resid 703 through 706 No H-bonds generated for 'chain 'B' and resid 703 through 706' Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.607A pdb=" N CYS B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 732 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 794 Processing helix chain 'B' and resid 799 through 827 removed outlier: 3.813A pdb=" N GLU B 803 " --> pdb=" O GLU B 799 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA B 804 " --> pdb=" O ASN B 800 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 805 " --> pdb=" O PHE B 801 " (cutoff:3.500A) removed outlier: 3.657A 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 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 835 through 860 removed outlier: 3.882A pdb=" N ALA B 840 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 875 Processing sheet with id= A, first strand: chain 'C' and resid 319 through 323 removed outlier: 6.767A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 79 through 81 removed outlier: 3.610A pdb=" N ALA D 73 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 111 through 113 removed outlier: 3.535A pdb=" N VAL D 112 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 178 through 180 removed outlier: 3.679A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 220 through 222 removed outlier: 4.156A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.960A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 252 " --> pdb=" O MET D 262 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 306 through 308 removed outlier: 4.006A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 46 through 52 removed outlier: 7.143A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N PHE D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER D 331 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.737A pdb=" N TYR A 95 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLY A 35 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL A 141 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU A 37 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.553A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 294 " --> pdb=" O VAL A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.623A pdb=" N GLY A 509 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= M, first strand: chain 'A' and resid 550 through 554 Processing sheet with id= N, first strand: chain 'A' and resid 589 through 591 Processing sheet with id= O, first strand: chain 'A' and resid 602 through 604 removed outlier: 3.592A pdb=" N ILE A 763 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.728A pdb=" N TYR B 95 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLY B 35 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL B 141 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU B 37 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.567A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'B' and resid 318 through 321 removed outlier: 3.588A pdb=" N GLY B 509 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 468 through 470 Processing sheet with id= T, first strand: chain 'B' and resid 550 through 554 Processing sheet with id= U, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= V, first strand: chain 'B' and resid 602 through 604 removed outlier: 3.736A pdb=" N ILE B 763 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 762 " --> pdb=" O ASN B 753 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 751 " --> pdb=" O THR B 764 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 7.79 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: 2887 1.32 - 1.44: 5110 1.44 - 1.57: 10126 1.57 - 1.70: 22 1.70 - 1.83: 136 Bond restraints: 18281 Sorted by residual: bond pdb=" C31 PCW B1402 " pdb=" O2 PCW B1402 " ideal model delta sigma weight residual 1.333 1.488 -0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" C31 PCW A1001 " pdb=" O2 PCW A1001 " ideal model delta sigma weight residual 1.333 1.485 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" C ASN B 802 " pdb=" O ASN B 802 " ideal model delta sigma weight residual 1.233 1.315 -0.082 1.29e-02 6.01e+03 4.09e+01 bond pdb=" C31 PCW B1402 " pdb=" C32 PCW B1402 " ideal model delta sigma weight residual 1.502 1.602 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C31 PCW A1001 " pdb=" C32 PCW A1001 " ideal model delta sigma weight residual 1.502 1.602 -0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 18276 not shown) Histogram of bond angle deviations from ideal: 99.79 - 110.41: 4390 110.41 - 121.02: 15245 121.02 - 131.64: 5111 131.64 - 142.26: 44 142.26 - 152.88: 2 Bond angle restraints: 24792 Sorted by residual: angle pdb=" C18 PCW B1402 " pdb=" C19 PCW B1402 " pdb=" C20 PCW B1402 " ideal model delta sigma weight residual 127.82 152.88 -25.06 3.00e+00 1.11e-01 6.98e+01 angle pdb=" C18 PCW A1001 " pdb=" C19 PCW A1001 " pdb=" C20 PCW A1001 " ideal model delta sigma weight residual 127.82 152.77 -24.95 3.00e+00 1.11e-01 6.92e+01 angle pdb=" N ASN A 118 " pdb=" CA ASN A 118 " pdb=" C ASN A 118 " ideal model delta sigma weight residual 112.38 104.38 8.00 1.22e+00 6.72e-01 4.30e+01 angle pdb=" C GLU A 232 " pdb=" N ARG A 233 " pdb=" CA ARG A 233 " ideal model delta sigma weight residual 122.65 113.56 9.09 1.60e+00 3.91e-01 3.23e+01 angle pdb=" N PHE A 714 " pdb=" CA PHE A 714 " pdb=" C PHE A 714 " ideal model delta sigma weight residual 113.38 106.41 6.97 1.23e+00 6.61e-01 3.21e+01 ... (remaining 24787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.83: 10219 20.83 - 41.67: 645 41.67 - 62.50: 85 62.50 - 83.34: 19 83.34 - 104.17: 7 Dihedral angle restraints: 10975 sinusoidal: 4430 harmonic: 6545 Sorted by residual: dihedral pdb=" CB CYS A 437 " pdb=" SG CYS A 437 " pdb=" SG CYS A 449 " pdb=" CB CYS A 449 " ideal model delta sinusoidal sigma weight residual 93.00 177.76 -84.76 1 1.00e+01 1.00e-02 8.72e+01 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 -167.54 81.54 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual -86.00 -39.73 -46.27 1 1.00e+01 1.00e-02 2.96e+01 ... (remaining 10972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.037: 2803 1.037 - 2.074: 0 2.074 - 3.111: 0 3.111 - 4.148: 0 4.148 - 5.185: 1 Chirality restraints: 2804 Sorted by residual: chirality pdb=" C2 PCW A1001 " pdb=" C1 PCW A1001 " pdb=" C3 PCW A1001 " pdb=" O2 PCW A1001 " both_signs ideal model delta sigma weight residual False -2.32 2.86 -5.19 2.00e-01 2.50e+01 6.72e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" C2 PCW B1402 " pdb=" C1 PCW B1402 " pdb=" C3 PCW B1402 " pdb=" O2 PCW B1402 " both_signs ideal model delta sigma weight residual False -2.32 -2.81 0.48 2.00e-01 2.50e+01 5.81e+00 ... (remaining 2801 not shown) Planarity restraints: 3127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.338 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG H 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.257 2.00e-02 2.50e+03 2.16e-01 5.81e+02 pdb=" C7 NAG H 1 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.362 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 817 " -0.026 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C VAL A 817 " 0.092 2.00e-02 2.50e+03 pdb=" O VAL A 817 " -0.034 2.00e-02 2.50e+03 pdb=" N ATRP A 818 " -0.032 2.00e-02 2.50e+03 ... (remaining 3124 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 57 2.56 - 3.14: 13438 3.14 - 3.73: 25428 3.73 - 4.31: 36179 4.31 - 4.90: 61491 Nonbonded interactions: 136593 Sorted by model distance: nonbonded pdb=" O LEU A 88 " pdb="CA CA A1003 " model vdw 1.971 2.510 nonbonded pdb=" O LEU B 88 " pdb="CA CA B1405 " model vdw 2.085 2.510 nonbonded pdb=" OE2 GLU C 318 " pdb=" OH TYR C 320 " model vdw 2.196 2.440 nonbonded pdb=" NH1 ARG A 69 " pdb=" O PRO A 407 " model vdw 2.203 2.520 nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.210 2.440 ... (remaining 136588 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 362 or resid 392 through 516 or (resid 517 and \ (name N or name CA or name C or name O or name CB )) or resid 518 through 586 or \ (resid 587 and (name N or name CA or name C or name O or name CB )) or resid 58 \ 8 through 601 or (resid 602 and (name N or name CA or name C or name O or name C \ B )) or resid 603 or (resid 604 and (name N or name CA or name C or name O or na \ me CB )) or resid 605 through 704 or (resid 705 and (name N or name CA or name C \ or name O or name CB )) or resid 706 through 708 or (resid 709 and (name N or n \ ame CA or name C or name O or name CB )) or resid 722 through 798 or (resid 799 \ and (name N or name CA or name C or name O or name CB )) or resid 800 through 81 \ 7 or resid 819 through 861 or (resid 862 through 863 and (name N or name CA or n \ ame C or name O or name CB )) or resid 864 through 865 or (resid 866 through 867 \ and (name N or name CA or name C or name O or name CB )) or resid 868 through 8 \ 70 or (resid 871 through 873 and (name N or name CA or name C or name O or name \ CB )) or resid 874 through 876 or resid 1002 through 1006)) selection = (chain 'B' and ((resid 20 and (name N or name CA or name C or name O or name CB \ )) or resid 21 through 47 or (resid 48 and (name N or name CA or name C or name \ O or name CB )) or resid 49 through 118 or (resid 119 through 135 and (name N or \ name CA or name C or name O or name CB )) or resid 136 through 361 or (resid 36 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 392 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 and (name N or name CA or name C o \ r name O or name CB )) or resid 593 through 817 or resid 819 through 876 or resi \ d 1404 through 1408)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.480 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: 24.780 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 52.550 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.120 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.155 18281 Z= 0.483 Angle : 0.966 25.057 24792 Z= 0.655 Chirality : 0.117 5.185 2804 Planarity : 0.008 0.293 3121 Dihedral : 13.695 104.170 6683 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.05 % Allowed : 1.61 % Favored : 98.34 % Cbeta Deviations : 0.09 % 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: 0.27 (0.18), residues: 2227 helix: 1.43 (0.18), residues: 871 sheet: -0.48 (0.26), residues: 383 loop : -0.63 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 719 HIS 0.007 0.001 HIS A 715 PHE 0.025 0.001 PHE A 814 TYR 0.038 0.001 TYR A 425 ARG 0.003 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 333 time to evaluate : 1.793 Fit side-chains revert: symmetry clash REVERT: C 230 TYR cc_start: 0.7454 (p90) cc_final: 0.7163 (p90) REVERT: A 58 VAL cc_start: 0.8667 (p) cc_final: 0.8424 (m) REVERT: A 189 ASN cc_start: 0.7770 (p0) cc_final: 0.7568 (p0) REVERT: A 410 ASP cc_start: 0.8131 (m-30) cc_final: 0.7834 (m-30) REVERT: A 663 SER cc_start: 0.8756 (t) cc_final: 0.8188 (p) REVERT: A 704 LEU cc_start: 0.8634 (tp) cc_final: 0.8293 (mt) REVERT: B 54 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7326 (ttm110) REVERT: B 58 VAL cc_start: 0.8156 (p) cc_final: 0.7943 (m) REVERT: B 251 GLU cc_start: 0.7293 (pt0) cc_final: 0.7063 (pt0) REVERT: B 341 LYS cc_start: 0.7588 (mtmt) cc_final: 0.7384 (mmtt) REVERT: B 357 ASN cc_start: 0.8375 (t0) cc_final: 0.8097 (t0) REVERT: B 643 VAL cc_start: 0.7562 (m) cc_final: 0.7337 (t) REVERT: B 706 PHE cc_start: 0.6185 (t80) cc_final: 0.5715 (t80) REVERT: B 771 MET cc_start: 0.5157 (mmm) cc_final: 0.4944 (mtt) outliers start: 1 outliers final: 1 residues processed: 334 average time/residue: 0.3310 time to fit residues: 161.8684 Evaluate side-chains 214 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 129 optimal weight: 0.6980 chunk 201 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS D 75 GLN D 175 GLN A 193 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 117 GLN B 463 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18281 Z= 0.177 Angle : 0.522 7.842 24792 Z= 0.279 Chirality : 0.042 0.177 2804 Planarity : 0.004 0.047 3121 Dihedral : 8.246 82.755 2751 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.96 % Allowed : 6.53 % Favored : 92.51 % 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: 0.41 (0.18), residues: 2227 helix: 1.69 (0.18), residues: 862 sheet: -0.39 (0.26), residues: 385 loop : -0.70 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 719 HIS 0.014 0.001 HIS A 766 PHE 0.028 0.001 PHE A 789 TYR 0.014 0.001 TYR B 421 ARG 0.007 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 217 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8086 (mtm180) cc_final: 0.7799 (mtm180) REVERT: C 230 TYR cc_start: 0.7524 (p90) cc_final: 0.7166 (p90) REVERT: C 295 THR cc_start: 0.7186 (OUTLIER) cc_final: 0.5908 (m) REVERT: D 188 MET cc_start: 0.8529 (mmm) cc_final: 0.8311 (mmm) REVERT: D 297 TRP cc_start: 0.8337 (m100) cc_final: 0.8076 (m100) REVERT: A 58 VAL cc_start: 0.8674 (p) cc_final: 0.8469 (m) REVERT: A 657 SER cc_start: 0.8692 (t) cc_final: 0.8483 (m) REVERT: A 663 SER cc_start: 0.8748 (t) cc_final: 0.8212 (p) REVERT: A 864 PRO cc_start: 0.8311 (Cg_endo) cc_final: 0.8093 (Cg_exo) REVERT: B 58 VAL cc_start: 0.8309 (p) cc_final: 0.7979 (m) REVERT: B 357 ASN cc_start: 0.8347 (t0) cc_final: 0.8067 (t0) REVERT: B 612 PHE cc_start: 0.7365 (t80) cc_final: 0.7158 (t80) REVERT: B 643 VAL cc_start: 0.7606 (m) cc_final: 0.7305 (t) REVERT: B 771 MET cc_start: 0.4738 (mmm) cc_final: 0.4493 (mtp) outliers start: 18 outliers final: 12 residues processed: 229 average time/residue: 0.3437 time to fit residues: 115.6585 Evaluate side-chains 206 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 55 optimal weight: 0.0010 chunk 201 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN A 193 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 735 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18281 Z= 0.180 Angle : 0.488 6.968 24792 Z= 0.260 Chirality : 0.042 0.190 2804 Planarity : 0.004 0.048 3121 Dihedral : 7.498 76.011 2751 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.39 % Allowed : 8.35 % Favored : 90.26 % 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: 0.46 (0.18), residues: 2227 helix: 1.74 (0.18), residues: 866 sheet: -0.30 (0.26), residues: 378 loop : -0.71 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 719 HIS 0.012 0.001 HIS A 766 PHE 0.021 0.001 PHE B 814 TYR 0.014 0.001 TYR B 421 ARG 0.004 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 206 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8094 (mtm180) cc_final: 0.7892 (mtm180) REVERT: C 230 TYR cc_start: 0.7526 (p90) cc_final: 0.7148 (p90) REVERT: D 181 THR cc_start: 0.8197 (p) cc_final: 0.7978 (t) REVERT: D 188 MET cc_start: 0.8536 (mmm) cc_final: 0.8318 (mmm) REVERT: A 657 SER cc_start: 0.8715 (t) cc_final: 0.8481 (m) REVERT: A 663 SER cc_start: 0.8719 (t) cc_final: 0.8194 (p) REVERT: B 58 VAL cc_start: 0.8321 (p) cc_final: 0.8002 (m) REVERT: B 357 ASN cc_start: 0.8334 (t0) cc_final: 0.8073 (t0) REVERT: B 643 VAL cc_start: 0.7596 (m) cc_final: 0.7312 (t) REVERT: B 771 MET cc_start: 0.4741 (mmm) cc_final: 0.4443 (mtp) outliers start: 26 outliers final: 17 residues processed: 220 average time/residue: 0.3217 time to fit residues: 106.0456 Evaluate side-chains 205 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 chunk 214 optimal weight: 0.6980 chunk 105 optimal weight: 0.0070 chunk 192 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18281 Z= 0.145 Angle : 0.460 7.704 24792 Z= 0.245 Chirality : 0.041 0.177 2804 Planarity : 0.004 0.047 3121 Dihedral : 7.046 70.032 2751 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.12 % Allowed : 9.90 % Favored : 88.98 % 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: 0.53 (0.18), residues: 2227 helix: 1.85 (0.18), residues: 863 sheet: -0.34 (0.26), residues: 386 loop : -0.70 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 719 HIS 0.011 0.001 HIS A 766 PHE 0.027 0.001 PHE A 789 TYR 0.012 0.001 TYR B 421 ARG 0.006 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.7360 (tt0) cc_final: 0.7155 (tt0) REVERT: C 230 TYR cc_start: 0.7485 (p90) cc_final: 0.7135 (p90) REVERT: D 181 THR cc_start: 0.8125 (p) cc_final: 0.7899 (t) REVERT: D 188 MET cc_start: 0.8528 (mmm) cc_final: 0.8317 (mmm) REVERT: D 297 TRP cc_start: 0.8296 (m100) cc_final: 0.8044 (m100) REVERT: A 570 ASP cc_start: 0.6293 (OUTLIER) cc_final: 0.6065 (t0) REVERT: A 657 SER cc_start: 0.8754 (t) cc_final: 0.8532 (m) REVERT: A 663 SER cc_start: 0.8694 (t) cc_final: 0.8180 (p) REVERT: B 58 VAL cc_start: 0.8303 (p) cc_final: 0.7994 (m) REVERT: B 357 ASN cc_start: 0.8296 (t0) cc_final: 0.8061 (t0) REVERT: B 643 VAL cc_start: 0.7595 (m) cc_final: 0.7291 (t) REVERT: B 688 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: B 771 MET cc_start: 0.4607 (mmm) cc_final: 0.4341 (mtp) REVERT: B 818 TRP cc_start: 0.8358 (m100) cc_final: 0.8115 (m100) outliers start: 21 outliers final: 16 residues processed: 199 average time/residue: 0.3390 time to fit residues: 100.0873 Evaluate side-chains 198 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 2.9990 chunk 121 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN A 309 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18281 Z= 0.224 Angle : 0.499 7.444 24792 Z= 0.265 Chirality : 0.042 0.281 2804 Planarity : 0.004 0.049 3121 Dihedral : 6.923 66.956 2751 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.28 % Allowed : 10.81 % Favored : 87.91 % 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: 0.38 (0.18), residues: 2227 helix: 1.71 (0.18), residues: 861 sheet: -0.46 (0.26), residues: 383 loop : -0.74 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 719 HIS 0.020 0.001 HIS B 463 PHE 0.019 0.001 PHE B 729 TYR 0.015 0.001 TYR B 421 ARG 0.004 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.7343 (tt0) cc_final: 0.7138 (tt0) REVERT: C 198 MET cc_start: 0.7695 (ttm) cc_final: 0.7451 (ttm) REVERT: A 570 ASP cc_start: 0.6406 (OUTLIER) cc_final: 0.6185 (t0) REVERT: A 657 SER cc_start: 0.8708 (t) cc_final: 0.8489 (m) REVERT: A 663 SER cc_start: 0.8710 (t) cc_final: 0.8188 (p) REVERT: A 716 ARG cc_start: 0.7369 (tpp-160) cc_final: 0.7031 (mmt-90) REVERT: A 789 PHE cc_start: 0.7345 (t80) cc_final: 0.6806 (t80) REVERT: B 58 VAL cc_start: 0.8355 (p) cc_final: 0.8048 (m) REVERT: B 357 ASN cc_start: 0.8299 (t0) cc_final: 0.8035 (t0) REVERT: B 643 VAL cc_start: 0.7608 (m) cc_final: 0.7330 (t) REVERT: B 688 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: B 771 MET cc_start: 0.4648 (mmm) cc_final: 0.4384 (mtp) REVERT: B 818 TRP cc_start: 0.8383 (m100) cc_final: 0.8158 (m100) outliers start: 24 outliers final: 16 residues processed: 200 average time/residue: 0.3427 time to fit residues: 103.1601 Evaluate side-chains 201 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 214 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 HIS B 90 ASN B 463 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18281 Z= 0.322 Angle : 0.558 7.656 24792 Z= 0.297 Chirality : 0.045 0.247 2804 Planarity : 0.004 0.051 3121 Dihedral : 7.051 63.402 2751 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.44 % Allowed : 11.82 % Favored : 86.73 % 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: 0.17 (0.18), residues: 2227 helix: 1.51 (0.18), residues: 862 sheet: -0.47 (0.26), residues: 381 loop : -0.88 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 719 HIS 0.011 0.001 HIS A 766 PHE 0.022 0.002 PHE A 814 TYR 0.019 0.002 TYR B 421 ARG 0.004 0.001 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.7323 (tt0) cc_final: 0.7101 (tt0) REVERT: A 570 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6391 (t0) REVERT: A 657 SER cc_start: 0.8656 (t) cc_final: 0.8429 (m) REVERT: A 663 SER cc_start: 0.8709 (t) cc_final: 0.8205 (p) REVERT: B 270 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8361 (t80) REVERT: B 357 ASN cc_start: 0.8340 (t0) cc_final: 0.8042 (t0) REVERT: B 643 VAL cc_start: 0.7621 (m) cc_final: 0.7371 (t) REVERT: B 688 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: B 771 MET cc_start: 0.4779 (mmm) cc_final: 0.4488 (mtp) REVERT: B 818 TRP cc_start: 0.8465 (m100) cc_final: 0.8179 (m100) outliers start: 27 outliers final: 19 residues processed: 210 average time/residue: 0.3316 time to fit residues: 103.8179 Evaluate side-chains 206 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 133 optimal weight: 0.0770 chunk 130 optimal weight: 0.9980 chunk 98 optimal weight: 0.0010 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN A 117 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 463 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18281 Z= 0.146 Angle : 0.474 7.187 24792 Z= 0.253 Chirality : 0.041 0.204 2804 Planarity : 0.004 0.048 3121 Dihedral : 6.701 62.859 2751 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.18 % Allowed : 12.41 % Favored : 86.41 % 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: 0.38 (0.18), residues: 2227 helix: 1.77 (0.18), residues: 859 sheet: -0.42 (0.27), residues: 378 loop : -0.80 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 99 HIS 0.019 0.001 HIS B 463 PHE 0.035 0.001 PHE A 789 TYR 0.018 0.001 TYR C 230 ARG 0.005 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.7294 (tt0) cc_final: 0.7062 (tt0) REVERT: C 29 LYS cc_start: 0.8501 (tptt) cc_final: 0.7828 (ttpp) REVERT: C 243 MET cc_start: 0.7380 (tpp) cc_final: 0.7074 (tpp) REVERT: A 570 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.6273 (t0) REVERT: A 657 SER cc_start: 0.8709 (t) cc_final: 0.8494 (m) REVERT: A 663 SER cc_start: 0.8728 (t) cc_final: 0.8186 (p) REVERT: B 357 ASN cc_start: 0.8310 (t0) cc_final: 0.8056 (t0) REVERT: B 643 VAL cc_start: 0.7621 (m) cc_final: 0.7346 (t) REVERT: B 688 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: B 771 MET cc_start: 0.4555 (mmm) cc_final: 0.4294 (mtp) REVERT: B 818 TRP cc_start: 0.8428 (m100) cc_final: 0.8158 (m100) outliers start: 22 outliers final: 13 residues processed: 200 average time/residue: 0.3447 time to fit residues: 101.1393 Evaluate side-chains 195 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 105 optimal weight: 0.0020 chunk 19 optimal weight: 2.9990 chunk 168 optimal weight: 0.0670 overall best weight: 0.7530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN A 117 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18281 Z= 0.183 Angle : 0.493 8.672 24792 Z= 0.262 Chirality : 0.042 0.198 2804 Planarity : 0.004 0.048 3121 Dihedral : 6.600 60.222 2751 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.23 % Allowed : 12.79 % Favored : 85.98 % 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: 0.38 (0.18), residues: 2227 helix: 1.75 (0.18), residues: 862 sheet: -0.43 (0.26), residues: 382 loop : -0.80 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 99 HIS 0.011 0.001 HIS A 766 PHE 0.039 0.001 PHE A 789 TYR 0.015 0.001 TYR C 230 ARG 0.006 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 183 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.8460 (tptt) cc_final: 0.7817 (ttpp) REVERT: C 290 TYR cc_start: 0.6546 (p90) cc_final: 0.6297 (p90) REVERT: A 657 SER cc_start: 0.8689 (t) cc_final: 0.8474 (m) REVERT: A 663 SER cc_start: 0.8710 (t) cc_final: 0.8187 (p) REVERT: B 357 ASN cc_start: 0.8303 (t0) cc_final: 0.8053 (t0) REVERT: B 643 VAL cc_start: 0.7640 (m) cc_final: 0.7376 (t) REVERT: B 688 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: B 771 MET cc_start: 0.4575 (mmm) cc_final: 0.4332 (mtp) REVERT: B 818 TRP cc_start: 0.8394 (m100) cc_final: 0.8137 (m100) REVERT: B 819 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8208 (tp) outliers start: 23 outliers final: 16 residues processed: 201 average time/residue: 0.3379 time to fit residues: 100.7836 Evaluate side-chains 198 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 180 optimal weight: 0.0570 chunk 188 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18281 Z= 0.163 Angle : 0.483 9.136 24792 Z= 0.254 Chirality : 0.041 0.187 2804 Planarity : 0.004 0.048 3121 Dihedral : 6.445 59.459 2751 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.02 % Allowed : 13.11 % Favored : 85.87 % 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: 0.45 (0.18), residues: 2227 helix: 1.81 (0.18), residues: 860 sheet: -0.39 (0.26), residues: 381 loop : -0.76 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 719 HIS 0.012 0.001 HIS A 766 PHE 0.039 0.001 PHE A 789 TYR 0.017 0.001 TYR A 744 ARG 0.007 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.8420 (tptt) cc_final: 0.7850 (ttpp) REVERT: C 230 TYR cc_start: 0.7365 (p90) cc_final: 0.7150 (p90) REVERT: D 80 ILE cc_start: 0.8249 (mt) cc_final: 0.8040 (mm) REVERT: A 657 SER cc_start: 0.8738 (t) cc_final: 0.8522 (m) REVERT: A 663 SER cc_start: 0.8711 (t) cc_final: 0.8190 (p) REVERT: A 873 ARG cc_start: 0.7531 (mtt180) cc_final: 0.7197 (mtt180) REVERT: B 357 ASN cc_start: 0.8278 (t0) cc_final: 0.7976 (t0) REVERT: B 643 VAL cc_start: 0.7675 (m) cc_final: 0.7407 (t) REVERT: B 688 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: B 819 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8184 (tp) outliers start: 19 outliers final: 16 residues processed: 199 average time/residue: 0.3492 time to fit residues: 102.8485 Evaluate side-chains 200 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 128 optimal weight: 0.0020 chunk 100 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 221 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 176 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN A 117 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 18281 Z= 0.154 Angle : 0.486 11.983 24792 Z= 0.258 Chirality : 0.041 0.197 2804 Planarity : 0.004 0.048 3121 Dihedral : 6.252 55.781 2751 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.02 % Allowed : 13.43 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2227 helix: 1.90 (0.18), residues: 852 sheet: -0.38 (0.27), residues: 381 loop : -0.74 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 719 HIS 0.012 0.001 HIS A 766 PHE 0.040 0.001 PHE A 789 TYR 0.015 0.001 TYR A 744 ARG 0.007 0.000 ARG B 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.8390 (tptt) cc_final: 0.7878 (ttpp) REVERT: D 80 ILE cc_start: 0.8240 (mt) cc_final: 0.8024 (mm) REVERT: A 657 SER cc_start: 0.8746 (t) cc_final: 0.8525 (m) REVERT: A 663 SER cc_start: 0.8688 (t) cc_final: 0.8181 (p) REVERT: A 873 ARG cc_start: 0.7527 (mtt180) cc_final: 0.7170 (mtt180) REVERT: B 357 ASN cc_start: 0.8232 (t0) cc_final: 0.7948 (t0) REVERT: B 643 VAL cc_start: 0.7673 (m) cc_final: 0.7398 (t) REVERT: B 688 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: B 818 TRP cc_start: 0.8324 (m100) cc_final: 0.8014 (m100) REVERT: B 819 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8182 (tp) outliers start: 19 outliers final: 17 residues processed: 202 average time/residue: 0.3494 time to fit residues: 103.9680 Evaluate side-chains 204 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 176 optimal weight: 0.0870 chunk 73 optimal weight: 0.6980 chunk 181 optimal weight: 0.0060 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.089603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.071913 restraints weight = 53885.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.071842 restraints weight = 46794.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072431 restraints weight = 43015.346| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 18281 Z= 0.154 Angle : 0.480 9.531 24792 Z= 0.254 Chirality : 0.041 0.194 2804 Planarity : 0.004 0.048 3121 Dihedral : 6.068 54.811 2751 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.07 % Allowed : 13.43 % Favored : 85.50 % 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: 0.54 (0.18), residues: 2227 helix: 1.89 (0.18), residues: 857 sheet: -0.31 (0.27), residues: 373 loop : -0.72 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 719 HIS 0.012 0.001 HIS A 766 PHE 0.043 0.001 PHE A 789 TYR 0.015 0.001 TYR A 744 ARG 0.007 0.000 ARG B 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3720.58 seconds wall clock time: 69 minutes 8.62 seconds (4148.62 seconds total)