Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 18 11:00:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/08_2023/7eoq_31227_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/08_2023/7eoq_31227.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/08_2023/7eoq_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_31227/08_2023/7eoq_31227_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/08_2023/7eoq_31227_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/08_2023/7eoq_31227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/08_2023/7eoq_31227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/08_2023/7eoq_31227_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eoq_31227/08_2023/7eoq_31227_trim_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 11.92, per 1000 atoms: 0.48 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: 10.31 Conformation dependent library (CDL) restraints added in 3.8 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: 5.35 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: 7.38 Time building geometry restraints manager: 11.02 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 - 21.97: 14453 21.97 - 43.95: 485 43.95 - 65.92: 28 65.92 - 87.90: 4 87.90 - 109.87: 10 Dihedral angle restraints: 14980 sinusoidal: 5874 harmonic: 9106 Sorted by residual: dihedral pdb=" C01 7RC C 902 " pdb=" C02 7RC C 902 " pdb=" N01 7RC C 902 " pdb=" C03 7RC C 902 " ideal model delta sinusoidal sigma weight residual 52.95 -56.92 109.87 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C01 7RC A 902 " pdb=" C02 7RC A 902 " pdb=" N01 7RC A 902 " pdb=" C03 7RC A 902 " ideal model delta sinusoidal sigma weight residual 52.95 -56.91 109.86 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C02 7RC C 902 " pdb=" C03 7RC C 902 " pdb=" N01 7RC C 902 " pdb=" C05 7RC C 902 " ideal model delta sinusoidal sigma weight residual 52.95 -56.90 109.85 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 14977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3068 0.046 - 0.092: 608 0.092 - 0.137: 223 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 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: 0.950 Set stop_for_unknowns flag: 0.010 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: 6.140 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 61.330 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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= 0.159 Angle : 0.470 9.860 34328 Z= 0.238 Chirality : 0.041 0.229 3904 Planarity : 0.003 0.060 4340 Dihedral : 10.226 109.871 9052 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.68 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 : 2.874 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: 0.3502 time to fit residues: 229.5089 Evaluate side-chains 234 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 2.757 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2024 time to fit residues: 5.5790 ------------------------------------------------------------------------------- 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: 0.7573 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 25302 Z= 0.162 Angle : 0.515 7.936 34328 Z= 0.260 Chirality : 0.042 0.322 3904 Planarity : 0.004 0.059 4340 Dihedral : 5.643 97.416 3370 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % 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: -0.11 (0.16), residues: 3112 helix: 1.70 (0.16), residues: 1154 sheet: -0.77 (0.30), residues: 340 loop : -1.28 (0.16), residues: 1618 *********************** 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 283 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.3207 time to fit residues: 150.5679 Evaluate side-chains 209 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.980 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3663 ------------------------------------------------------------------------------- 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: 20.0000 chunk 192 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 0.5980 chunk 306 optimal weight: 7.9990 chunk 252 optimal weight: 1.9990 chunk 281 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 147 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 147 GLN D 477 HIS ** D 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7854 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 25302 Z= 0.284 Angle : 0.594 7.959 34328 Z= 0.308 Chirality : 0.044 0.294 3904 Planarity : 0.004 0.052 4340 Dihedral : 5.027 89.784 3370 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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: -0.45 (0.16), residues: 3112 helix: 1.20 (0.16), residues: 1190 sheet: -1.04 (0.29), residues: 368 loop : -1.33 (0.16), residues: 1554 *********************** 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 248 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.723 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3292 time to fit residues: 136.1114 Evaluate side-chains 178 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 3.077 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9093 ------------------------------------------------------------------------------- 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: 3.9990 chunk 147 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 284 optimal weight: 0.0670 chunk 301 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 269 optimal weight: 0.0060 chunk 81 optimal weight: 0.0970 overall best weight: 0.6134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 153 GLN B 134 HIS B 477 HIS ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 153 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN 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: 0.7758 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 25302 Z= 0.126 Angle : 0.498 9.018 34328 Z= 0.252 Chirality : 0.042 0.320 3904 Planarity : 0.003 0.052 4340 Dihedral : 4.676 81.949 3370 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % 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: -0.34 (0.16), residues: 3112 helix: 1.22 (0.16), residues: 1188 sheet: -1.01 (0.29), residues: 370 loop : -1.18 (0.16), residues: 1554 *********************** 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 251 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 3.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3369 time to fit residues: 139.3353 Evaluate side-chains 184 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.026 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0458 ------------------------------------------------------------------------------- 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: 0.9990 chunk 171 optimal weight: 0.9990 chunk 4 optimal weight: 30.0000 chunk 224 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 257 optimal weight: 0.4980 chunk 208 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 153 optimal weight: 0.1980 chunk 270 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 154 GLN B 780 HIS ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 477 HIS ** D 521 ASN ** 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: 0.7745 moved from start: 0.2991 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= 0.121 Angle : 0.485 7.967 34328 Z= 0.246 Chirality : 0.042 0.330 3904 Planarity : 0.003 0.052 4340 Dihedral : 4.495 77.658 3370 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.37 (0.16), residues: 3112 helix: 1.12 (0.15), residues: 1182 sheet: -0.87 (0.30), residues: 352 loop : -1.16 (0.16), residues: 1578 *********************** 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 257 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.3147 time to fit residues: 136.2902 Evaluate side-chains 196 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 3.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8565 ------------------------------------------------------------------------------- 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: 4.9990 chunk 271 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 177 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 301 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 139 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 99 optimal weight: 0.0070 chunk 158 optimal weight: 0.0870 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3029 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= 0.115 Angle : 0.505 8.738 34328 Z= 0.252 Chirality : 0.042 0.330 3904 Planarity : 0.003 0.052 4340 Dihedral : 4.399 73.572 3370 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % 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: -0.38 (0.16), residues: 3112 helix: 1.12 (0.16), residues: 1180 sheet: -0.89 (0.29), residues: 374 loop : -1.17 (0.16), residues: 1558 *********************** 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 262 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3240 time to fit residues: 143.2078 Evaluate side-chains 202 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 3.191 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2081 ------------------------------------------------------------------------------- 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: 7.9990 chunk 34 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 300 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 183 optimal weight: 30.0000 chunk 138 optimal weight: 10.0000 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 521 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 25302 Z= 0.305 Angle : 0.618 8.601 34328 Z= 0.318 Chirality : 0.044 0.315 3904 Planarity : 0.004 0.050 4340 Dihedral : 5.045 75.276 3370 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % 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: -0.60 (0.16), residues: 3112 helix: 0.93 (0.15), residues: 1208 sheet: -0.76 (0.29), residues: 368 loop : -1.41 (0.16), residues: 1536 *********************** 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 220 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.883 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.3180 time to fit residues: 117.7841 Evaluate side-chains 162 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.888 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8703 ------------------------------------------------------------------------------- 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: 5.9990 chunk 120 optimal weight: 0.1980 chunk 179 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 chunk 236 optimal weight: 6.9990 overall best weight: 2.0582 ------------------------------------------------------------------------------- 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 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 201 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 25302 Z= 0.174 Angle : 0.543 7.969 34328 Z= 0.276 Chirality : 0.043 0.341 3904 Planarity : 0.003 0.050 4340 Dihedral : 4.871 70.750 3370 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.06 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 : 0.03 % 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: -0.54 (0.16), residues: 3112 helix: 1.00 (0.16), residues: 1182 sheet: -0.97 (0.28), residues: 390 loop : -1.27 (0.17), residues: 1540 *********************** 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 221 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3305 time to fit residues: 121.7564 Evaluate side-chains 175 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.934 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8827 ------------------------------------------------------------------------------- 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: 0.7980 chunk 288 optimal weight: 7.9990 chunk 262 optimal weight: 0.0980 chunk 280 optimal weight: 20.0000 chunk 168 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 265 optimal weight: 8.9990 chunk 279 optimal weight: 0.0070 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 GLN C 153 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4023 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= 0.131 Angle : 0.532 8.326 34328 Z= 0.269 Chirality : 0.043 0.380 3904 Planarity : 0.003 0.052 4340 Dihedral : 4.636 66.900 3370 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % 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: -0.51 (0.16), residues: 3112 helix: 0.98 (0.16), residues: 1182 sheet: -0.86 (0.29), residues: 382 loop : -1.25 (0.17), residues: 1548 *********************** 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 228 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.933 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3295 time to fit residues: 126.6038 Evaluate side-chains 184 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.943 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1691 ------------------------------------------------------------------------------- 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: 0.1980 chunk 296 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 310 optimal weight: 0.2980 chunk 286 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 191 optimal weight: 0.0470 chunk 151 optimal weight: 0.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- 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 ** 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: 0.7837 moved from start: 0.4044 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= 0.127 Angle : 0.533 11.731 34328 Z= 0.267 Chirality : 0.043 0.357 3904 Planarity : 0.003 0.079 4340 Dihedral : 4.566 63.985 3370 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.54 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: -0.54 (0.16), residues: 3112 helix: 0.96 (0.16), residues: 1182 sheet: -0.86 (0.28), residues: 392 loop : -1.27 (0.16), residues: 1538 ********************** 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 228 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.709 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3349 time to fit residues: 129.5537 Evaluate side-chains 184 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0963 ------------------------------------------------------------------------------- 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: 6.9990 chunk 263 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 228 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 247 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.0040 overall best weight: 0.8794 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.065402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.053672 restraints weight = 159041.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.054829 restraints weight = 101135.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.055609 restraints weight = 73930.500| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4073 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= 0.128 Angle : 0.524 8.211 34328 Z= 0.264 Chirality : 0.043 0.347 3904 Planarity : 0.003 0.052 4340 Dihedral : 4.493 62.946 3370 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.47 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: -0.51 (0.16), residues: 3112 helix: 1.00 (0.16), residues: 1178 sheet: -0.89 (0.29), residues: 378 loop : -1.26 (0.16), residues: 1556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4101.32 seconds wall clock time: 76 minutes 35.15 seconds (4595.15 seconds total)