Starting phenix.real_space_refine (version: dev) on Thu Dec 15 08:07:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/12_2022/7eoq_31227_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/12_2022/7eoq_31227.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/12_2022/7eoq_31227_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/12_2022/7eoq_31227_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/12_2022/7eoq_31227_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/12_2022/7eoq_31227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/12_2022/7eoq_31227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/12_2022/7eoq_31227_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/12_2022/7eoq_31227_trim_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 24742 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6111 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 31, 'TRANS': 751} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 6188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6188 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 6111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6111 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 31, 'TRANS': 751} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 6188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6188 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'7RC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'7RC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 13.29, per 1000 atoms: 0.54 Number of scatterers: 24742 At special positions: 0 Unit cell: (114.582, 145.002, 188.604, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 2 15.00 O 4590 8.00 N 4160 7.00 C 15838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS D 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS C 794 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 798 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 687 " " NAG B 901 " - " ASN B 276 " " NAG B 902 " - " ASN B 771 " " NAG B 903 " - " ASN B 471 " " NAG C 901 " - " ASN C 687 " " NAG D 901 " - " ASN D 276 " " NAG D 902 " - " ASN D 771 " " NAG D 903 " - " ASN D 471 " Time building additional restraints: 9.77 Conformation dependent library (CDL) restraints added in 3.5 seconds 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 26 sheets defined 36.8% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.804A pdb=" N HIS A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 removed outlier: 4.059A pdb=" N THR A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 157 " --> pdb=" O GLN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 233 through 246 removed outlier: 3.536A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 309 removed outlier: 3.667A pdb=" N LYS A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.857A pdb=" N ARG A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'A' and resid 518 through 521 No H-bonds generated for 'chain 'A' and resid 518 through 521' Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.907A pdb=" N LEU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 611 removed outlier: 4.449A pdb=" N ILE A 605 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 651 removed outlier: 3.627A pdb=" N VAL A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL A 633 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 671 No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 673 through 675 No H-bonds generated for 'chain 'A' and resid 673 through 675' Processing helix chain 'A' and resid 689 through 695 Processing helix chain 'A' and resid 699 through 707 removed outlier: 4.277A pdb=" N GLN A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR A 704 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 772 through 785 removed outlier: 4.158A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.601A pdb=" N CYS A 794 " --> pdb=" O GLU A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 836 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 71 through 81 Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.940A pdb=" N PHE B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 158 Processing helix chain 'B' and resid 171 through 187 removed outlier: 4.455A pdb=" N GLU B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 256 through 259 Processing helix chain 'B' and resid 278 through 298 removed outlier: 3.845A pdb=" N SER B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 3.516A pdb=" N LYS B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 470 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 521 through 526 removed outlier: 3.758A pdb=" N TYR B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 582 removed outlier: 3.645A pdb=" N TRP B 563 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 614 removed outlier: 3.874A pdb=" N LEU B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 655 removed outlier: 3.885A pdb=" N MET B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 673 No H-bonds generated for 'chain 'B' and resid 670 through 673' Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.971A pdb=" N ARG B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 722 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.659A pdb=" N PHE B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 781 Processing helix chain 'B' and resid 784 through 791 Processing helix chain 'B' and resid 811 through 842 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.803A pdb=" N HIS C 119 " --> pdb=" O PHE C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 165 removed outlier: 4.058A pdb=" N THR C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 215 through 220 Processing helix chain 'C' and resid 233 through 246 removed outlier: 3.537A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 309 removed outlier: 3.667A pdb=" N LYS C 309 " --> pdb=" O SER C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 471 removed outlier: 3.856A pdb=" N ARG C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'C' and resid 518 through 521 No H-bonds generated for 'chain 'C' and resid 518 through 521' Processing helix chain 'C' and resid 561 through 580 removed outlier: 3.912A pdb=" N LEU C 566 " --> pdb=" O PHE C 562 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 611 removed outlier: 4.449A pdb=" N ILE C 605 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 651 removed outlier: 3.631A pdb=" N VAL C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL C 633 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP C 634 " --> pdb=" O MET C 630 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA C 635 " --> pdb=" O VAL C 631 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE C 637 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 671 No H-bonds generated for 'chain 'C' and resid 668 through 671' Processing helix chain 'C' and resid 673 through 675 No H-bonds generated for 'chain 'C' and resid 673 through 675' Processing helix chain 'C' and resid 689 through 695 Processing helix chain 'C' and resid 699 through 707 removed outlier: 4.277A pdb=" N GLN C 703 " --> pdb=" O PRO C 699 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR C 704 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS C 707 " --> pdb=" O GLN C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 772 through 785 removed outlier: 4.157A pdb=" N LEU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 removed outlier: 3.604A pdb=" N CYS C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 836 Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'D' and resid 71 through 81 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 105 through 113 removed outlier: 3.940A pdb=" N PHE D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 158 Processing helix chain 'D' and resid 171 through 187 removed outlier: 4.449A pdb=" N GLU D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 225 through 237 Processing helix chain 'D' and resid 252 through 254 No H-bonds generated for 'chain 'D' and resid 252 through 254' Processing helix chain 'D' and resid 256 through 259 Processing helix chain 'D' and resid 278 through 298 removed outlier: 3.843A pdb=" N SER D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 removed outlier: 3.516A pdb=" N LYS D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 521 through 526 removed outlier: 3.756A pdb=" N TYR D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 582 removed outlier: 3.643A pdb=" N TRP D 563 " --> pdb=" O SER D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 614 removed outlier: 3.873A pdb=" N LEU D 614 " --> pdb=" O SER D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 655 removed outlier: 3.887A pdb=" N MET D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE D 643 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 673 No H-bonds generated for 'chain 'D' and resid 670 through 673' Processing helix chain 'D' and resid 688 through 695 Processing helix chain 'D' and resid 700 through 708 removed outlier: 3.964A pdb=" N ARG D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS D 708 " --> pdb=" O ARG D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 722 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.658A pdb=" N PHE D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 781 Processing helix chain 'D' and resid 784 through 791 Processing helix chain 'D' and resid 811 through 842 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 38 removed outlier: 6.603A pdb=" N GLY A 97 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 125 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 100 " --> pdb=" O LEU A 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 172 through 174 removed outlier: 7.020A pdb=" N VAL A 173 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU A 228 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE A 254 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU A 229 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ILE A 256 " --> pdb=" O LEU A 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 277 through 280 removed outlier: 3.523A pdb=" N SER A 280 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 365 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 373 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 405 through 409 removed outlier: 6.839A pdb=" N THR A 474 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE A 408 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASP A 476 " --> pdb=" O ILE A 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 434 through 439 removed outlier: 3.815A pdb=" N LYS A 438 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 452 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 533 through 537 Processing sheet with id= G, first strand: chain 'B' and resid 30 through 32 removed outlier: 4.160A pdb=" N GLY B 30 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL B 92 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU B 119 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 194 through 197 removed outlier: 6.724A pdb=" N LEU B 165 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 197 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 167 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 164 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 220 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 222 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER B 168 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 246 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU B 221 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 248 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 267 through 271 removed outlier: 3.941A pdb=" N GLY B 365 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 399 through 402 removed outlier: 5.747A pdb=" N GLU B 475 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR B 402 " --> pdb=" O GLU B 475 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS B 477 " --> pdb=" O THR B 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 409 through 412 removed outlier: 3.519A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 512 through 514 Processing sheet with id= M, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.986A pdb=" N TRP B 731 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 36 through 38 removed outlier: 6.603A pdb=" N GLY C 97 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU C 125 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 172 through 174 removed outlier: 7.017A pdb=" N VAL C 173 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU C 228 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE C 254 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N LEU C 229 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ILE C 256 " --> pdb=" O LEU C 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 277 through 280 removed outlier: 3.526A pdb=" N SER C 280 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 365 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 405 through 409 removed outlier: 6.839A pdb=" N THR C 474 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE C 408 " --> pdb=" O THR C 474 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP C 476 " --> pdb=" O ILE C 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 434 through 439 removed outlier: 3.811A pdb=" N LYS C 438 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 452 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 533 through 537 Processing sheet with id= T, first strand: chain 'D' and resid 30 through 32 removed outlier: 4.160A pdb=" N GLY D 30 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL D 92 " --> pdb=" O PRO D 117 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU D 119 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.725A pdb=" N LEU D 165 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE D 197 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL D 167 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D 164 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 220 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 222 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL D 246 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU D 221 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU D 248 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 267 through 271 removed outlier: 3.948A pdb=" N GLY D 365 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 399 through 402 removed outlier: 5.746A pdb=" N GLU D 475 " --> pdb=" O ILE D 400 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR D 402 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N HIS D 477 " --> pdb=" O THR D 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 409 through 412 removed outlier: 3.518A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 512 through 514 Processing sheet with id= Z, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.987A pdb=" N TRP D 731 " --> pdb=" O THR D 539 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2094 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: 7.39 Time building geometry restraints manager: 10.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7937 1.34 - 1.46: 4653 1.46 - 1.58: 12446 1.58 - 1.70: 4 1.70 - 1.81: 262 Bond restraints: 25302 Sorted by residual: bond pdb=" O02 7RC C 902 " pdb=" P01 7RC C 902 " ideal model delta sigma weight residual 1.510 1.610 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O02 7RC A 902 " pdb=" P01 7RC A 902 " ideal model delta sigma weight residual 1.510 1.610 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" O03 7RC A 902 " pdb=" P01 7RC A 902 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O03 7RC C 902 " pdb=" P01 7RC C 902 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C08 7RC C 902 " pdb=" O01 7RC C 902 " ideal model delta sigma weight residual 1.259 1.356 -0.097 2.00e-02 2.50e+03 2.33e+01 ... (remaining 25297 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.14: 779 107.14 - 113.87: 14357 113.87 - 120.60: 9708 120.60 - 127.33: 9174 127.33 - 134.06: 310 Bond angle restraints: 34328 Sorted by residual: angle pdb=" C LEU A 512 " pdb=" CA LEU A 512 " pdb=" CB LEU A 512 " ideal model delta sigma weight residual 109.64 119.50 -9.86 1.77e+00 3.19e-01 3.10e+01 angle pdb=" C LEU C 512 " pdb=" CA LEU C 512 " pdb=" CB LEU C 512 " ideal model delta sigma weight residual 109.64 117.83 -8.19 1.77e+00 3.19e-01 2.14e+01 angle pdb=" N CYS B 698 " pdb=" CA CYS B 698 " pdb=" C CYS B 698 " ideal model delta sigma weight residual 114.56 109.06 5.50 1.27e+00 6.20e-01 1.88e+01 angle pdb=" N CYS D 698 " pdb=" CA CYS D 698 " pdb=" C CYS D 698 " ideal model delta sigma weight residual 114.56 109.07 5.49 1.27e+00 6.20e-01 1.87e+01 angle pdb=" N THR A 513 " pdb=" CA THR A 513 " pdb=" C THR A 513 " ideal model delta sigma weight residual 110.42 103.83 6.59 1.55e+00 4.16e-01 1.81e+01 ... (remaining 34323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 14267 17.62 - 35.24: 632 35.24 - 52.86: 115 52.86 - 70.48: 10 70.48 - 88.10: 4 Dihedral angle restraints: 15028 sinusoidal: 5922 harmonic: 9106 Sorted by residual: dihedral pdb=" CA MET B 576 " pdb=" CB MET B 576 " pdb=" CG MET B 576 " pdb=" SD MET B 576 " ideal model delta sinusoidal sigma weight residual -60.00 -115.58 55.58 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA MET D 576 " pdb=" CB MET D 576 " pdb=" CG MET D 576 " pdb=" SD MET D 576 " ideal model delta sinusoidal sigma weight residual -60.00 -114.80 54.80 3 1.50e+01 4.44e-03 9.31e+00 dihedral pdb=" N MET D 502 " pdb=" CA MET D 502 " pdb=" CB MET D 502 " pdb=" CG MET D 502 " ideal model delta sinusoidal sigma weight residual -180.00 -125.22 -54.78 3 1.50e+01 4.44e-03 9.31e+00 ... (remaining 15025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3080 0.046 - 0.092: 599 0.092 - 0.137: 220 0.137 - 0.183: 3 0.183 - 0.229: 2 Chirality restraints: 3904 Sorted by residual: chirality pdb=" C1 NAG D 902 " pdb=" ND2 ASN D 771 " pdb=" C2 NAG D 902 " pdb=" O5 NAG D 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C1 NAG B 902 " pdb=" ND2 ASN B 771 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 471 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 3901 not shown) Planarity restraints: 4348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 94 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO B 95 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 94 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO D 95 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 55 " 0.008 2.00e-02 2.50e+03 6.19e-03 9.57e-01 pdb=" CG TRP A 55 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 55 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 55 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 55 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 55 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 55 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 55 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 55 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 55 " -0.000 2.00e-02 2.50e+03 ... (remaining 4345 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1558 2.74 - 3.28: 25810 3.28 - 3.82: 40625 3.82 - 4.36: 45586 4.36 - 4.90: 76874 Nonbonded interactions: 190453 Sorted by model distance: nonbonded pdb=" OG1 THR C 531 " pdb=" OD1 ASP C 731 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR A 531 " pdb=" OD1 ASP A 731 " model vdw 2.196 2.440 nonbonded pdb=" O LYS C 465 " pdb=" OG SER C 468 " model vdw 2.232 2.440 nonbonded pdb=" O LYS A 465 " pdb=" OG SER A 468 " model vdw 2.233 2.440 nonbonded pdb=" O ASN B 50 " pdb=" NE2 GLN B 59 " model vdw 2.254 2.520 ... (remaining 190448 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 152 5.16 5 C 15838 2.51 5 N 4160 2.21 5 O 4590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.740 Check model and map are aligned: 0.370 Convert atoms to be neutral: 0.190 Process input model: 58.890 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.002 0.100 25302 Z= 0.147 Angle : 0.462 9.860 34328 Z= 0.236 Chirality : 0.040 0.229 3904 Planarity : 0.003 0.060 4340 Dihedral : 9.714 88.103 9100 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 2.14 % 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: 0.09 (0.16), residues: 3112 helix: 1.96 (0.16), residues: 1200 sheet: -0.84 (0.32), residues: 302 loop : -1.30 (0.16), residues: 1610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 372 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 5 residues processed: 417 average time/residue: 0.3511 time to fit residues: 230.0593 Evaluate side-chains 234 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 3.193 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2123 time to fit residues: 6.0163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 80 optimal weight: 0.1980 chunk 159 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 283 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 432 ASN A 674 HIS B 134 HIS B 477 HIS C 153 GLN C 154 GLN C 432 ASN C 674 HIS ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 477 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 25302 Z= 0.159 Angle : 0.509 7.884 34328 Z= 0.259 Chirality : 0.042 0.298 3904 Planarity : 0.004 0.057 4340 Dihedral : 3.875 77.301 3418 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.00 % 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: -0.12 (0.16), residues: 3112 helix: 1.70 (0.16), residues: 1152 sheet: -0.70 (0.30), residues: 350 loop : -1.31 (0.16), residues: 1610 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3211 time to fit residues: 150.0854 Evaluate side-chains 208 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 235 optimal weight: 8.9990 chunk 192 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 283 optimal weight: 0.2980 chunk 306 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN B 134 HIS B 147 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 153 GLN D 134 HIS D 147 GLN D 477 HIS ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25302 Z= 0.189 Angle : 0.511 8.011 34328 Z= 0.264 Chirality : 0.042 0.331 3904 Planarity : 0.004 0.051 4340 Dihedral : 4.109 79.091 3418 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.00 % 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: -0.23 (0.16), residues: 3112 helix: 1.47 (0.16), residues: 1180 sheet: -0.88 (0.29), residues: 368 loop : -1.27 (0.16), residues: 1564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.3058 time to fit residues: 135.0129 Evaluate side-chains 192 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.877 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 7.9990 chunk 213 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 31 optimal weight: 0.0000 chunk 135 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 301 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 269 optimal weight: 9.9990 chunk 81 optimal weight: 0.0070 overall best weight: 2.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 153 GLN B 134 HIS B 477 HIS ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 134 HIS D 477 HIS ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 25302 Z= 0.183 Angle : 0.515 10.557 34328 Z= 0.263 Chirality : 0.043 0.366 3904 Planarity : 0.003 0.051 4340 Dihedral : 4.330 83.968 3418 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 0.00 % 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: -0.31 (0.16), residues: 3112 helix: 1.28 (0.16), residues: 1190 sheet: -1.00 (0.29), residues: 370 loop : -1.19 (0.17), residues: 1552 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.3151 time to fit residues: 128.8720 Evaluate side-chains 186 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.987 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 4 optimal weight: 30.0000 chunk 224 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 257 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 153 optimal weight: 20.0000 chunk 270 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 780 HIS ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN D 134 HIS D 477 HIS ** D 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 780 HIS ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 25302 Z= 0.309 Angle : 0.618 7.916 34328 Z= 0.321 Chirality : 0.044 0.412 3904 Planarity : 0.004 0.050 4340 Dihedral : 5.020 84.584 3418 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 3112 helix: 0.84 (0.15), residues: 1202 sheet: -0.97 (0.28), residues: 382 loop : -1.45 (0.17), residues: 1528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.3232 time to fit residues: 118.6306 Evaluate side-chains 168 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 8.9990 chunk 271 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 301 optimal weight: 0.0370 chunk 250 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 overall best weight: 2.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 648 ASN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 119 HIS C 153 GLN C 323 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 25302 Z= 0.180 Angle : 0.538 9.705 34328 Z= 0.276 Chirality : 0.043 0.388 3904 Planarity : 0.003 0.052 4340 Dihedral : 4.800 74.148 3418 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 3112 helix: 1.01 (0.16), residues: 1178 sheet: -1.02 (0.28), residues: 372 loop : -1.33 (0.16), residues: 1562 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 3.297 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.3306 time to fit residues: 121.9083 Evaluate side-chains 173 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 220 optimal weight: 0.4980 chunk 170 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 300 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 25302 Z= 0.181 Angle : 0.528 7.866 34328 Z= 0.270 Chirality : 0.043 0.375 3904 Planarity : 0.003 0.052 4340 Dihedral : 4.720 63.269 3418 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.16), residues: 3112 helix: 1.06 (0.16), residues: 1180 sheet: -0.97 (0.27), residues: 402 loop : -1.33 (0.17), residues: 1530 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.950 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3308 time to fit residues: 120.1313 Evaluate side-chains 174 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 3.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.8980 chunk 120 optimal weight: 0.0970 chunk 179 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 chunk 236 optimal weight: 9.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 153 GLN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 25302 Z= 0.128 Angle : 0.531 8.682 34328 Z= 0.267 Chirality : 0.043 0.371 3904 Planarity : 0.004 0.071 4340 Dihedral : 4.573 54.755 3418 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.16), residues: 3112 helix: 0.99 (0.16), residues: 1180 sheet: -0.90 (0.28), residues: 390 loop : -1.29 (0.17), residues: 1542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.995 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.3334 time to fit residues: 122.1829 Evaluate side-chains 175 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.2980 chunk 288 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 chunk 280 optimal weight: 0.8980 chunk 168 optimal weight: 0.3980 chunk 122 optimal weight: 0.0970 chunk 220 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 25302 Z= 0.137 Angle : 0.523 8.085 34328 Z= 0.264 Chirality : 0.043 0.357 3904 Planarity : 0.003 0.053 4340 Dihedral : 4.485 59.057 3418 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.55 (0.16), residues: 3112 helix: 1.00 (0.16), residues: 1176 sheet: -0.82 (0.28), residues: 394 loop : -1.33 (0.17), residues: 1542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.940 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.3265 time to fit residues: 117.6880 Evaluate side-chains 170 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 3.168 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.9990 chunk 296 optimal weight: 0.0970 chunk 180 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 310 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN B 556 GLN ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 25302 Z= 0.176 Angle : 0.541 8.408 34328 Z= 0.274 Chirality : 0.043 0.352 3904 Planarity : 0.004 0.061 4340 Dihedral : 4.447 49.216 3418 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.16), residues: 3112 helix: 1.07 (0.16), residues: 1176 sheet: -0.94 (0.28), residues: 394 loop : -1.28 (0.17), residues: 1542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.465 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3320 time to fit residues: 119.5099 Evaluate side-chains 173 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 3.685 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 228 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.061339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.049296 restraints weight = 161038.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.050371 restraints weight = 103046.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.051098 restraints weight = 76247.739| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 25302 Z= 0.269 Angle : 0.602 8.656 34328 Z= 0.310 Chirality : 0.045 0.395 3904 Planarity : 0.004 0.084 4340 Dihedral : 4.793 35.935 3418 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 3112 helix: 0.90 (0.15), residues: 1190 sheet: -1.07 (0.26), residues: 430 loop : -1.53 (0.17), residues: 1492 =============================================================================== Job complete usr+sys time: 3843.42 seconds wall clock time: 72 minutes 30.30 seconds (4350.30 seconds total)