Starting phenix.real_space_refine on Fri Sep 19 05:37:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c60_45239/09_2025/9c60_45239.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c60_45239/09_2025/9c60_45239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c60_45239/09_2025/9c60_45239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c60_45239/09_2025/9c60_45239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c60_45239/09_2025/9c60_45239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c60_45239/09_2025/9c60_45239.map" } resolution = 3.8 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 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= 0.002 sd= 0.059 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 15248 2.51 5 N 3932 2.21 5 O 4453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23759 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5848 Classifications: {'peptide': 738} Link IDs: {'PTRANS': 27, 'TRANS': 710} Chain breaks: 2 Chain: "B" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5953 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 723} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5922 Classifications: {'peptide': 748} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 5868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5868 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 713} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.18, per 1000 atoms: 0.26 Number of scatterers: 23759 At special positions: 0 Unit cell: (120.84, 159, 186.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 4453 8.00 N 3932 7.00 C 15248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.04 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 A1001 " - " ASN A 275 " " NAG A1002 " - " ASN A 412 " " NAG A1003 " - " ASN A 546 " " NAG B1001 " - " ASN B 412 " " NAG B1002 " - " ASN B 546 " " NAG B1003 " - " ASN B 751 " " NAG C1001 " - " ASN C 751 " " NAG C1002 " - " ASN C 412 " " NAG C1003 " - " ASN C 546 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG D1003 " - " ASN D 546 " Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 33 sheets defined 47.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 111 through 126 removed outlier: 4.132A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.222A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.562A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.514A pdb=" N GLY A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.519A pdb=" N TYR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 317 through 336 Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 560 through 582 Processing helix chain 'A' and resid 632 through 665 removed outlier: 4.001A pdb=" N GLU A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 677 removed outlier: 3.561A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 696 removed outlier: 3.848A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 Processing helix chain 'A' and resid 720 through 730 removed outlier: 4.552A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 774 through 789 removed outlier: 3.689A pdb=" N ILE A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 802 removed outlier: 3.748A pdb=" N MET A 793 " --> pdb=" O GLY A 789 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN A 802 " --> pdb=" O TRP A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 834 removed outlier: 4.050A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.578A pdb=" N ALA B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 Processing helix chain 'B' and resid 152 through 167 removed outlier: 4.427A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.065A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.875A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 244 removed outlier: 3.535A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 317 through 336 Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 501 through 507 removed outlier: 3.733A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 551 through 557 removed outlier: 4.322A pdb=" N PHE B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 Processing helix chain 'B' and resid 634 through 662 Processing helix chain 'B' and resid 670 through 677 Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 699 through 712 removed outlier: 4.177A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.739A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 Processing helix chain 'B' and resid 774 through 788 removed outlier: 3.735A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 4.346A pdb=" N TRP B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP B 799 " --> pdb=" O LYS B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 842 removed outlier: 3.754A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.644A pdb=" N ASN C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 101 removed outlier: 3.625A pdb=" N LEU C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 removed outlier: 4.088A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 4.171A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 195 Proline residue: C 192 - end of helix Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 231 through 244 Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.758A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 306 through 310 removed outlier: 4.540A pdb=" N GLY C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 335 Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 454 through 457 removed outlier: 3.865A pdb=" N ASP C 457 " --> pdb=" O TYR C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 462 through 474 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.703A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 4.118A pdb=" N VAL C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 560 through 584 Processing helix chain 'C' and resid 631 through 665 removed outlier: 4.312A pdb=" N GLU C 662 " --> pdb=" O PHE C 658 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 665 " --> pdb=" O VAL C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 677 Processing helix chain 'C' and resid 691 through 696 Processing helix chain 'C' and resid 699 through 712 Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 749 Processing helix chain 'C' and resid 773 through 789 removed outlier: 3.748A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 removed outlier: 3.610A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 836 removed outlier: 3.992A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 101 removed outlier: 3.506A pdb=" N LEU D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 152 through 168 removed outlier: 4.332A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 185 through 195 Proline residue: D 192 - end of helix Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.737A pdb=" N GLY D 273 " --> pdb=" O ARG D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.945A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 removed outlier: 3.904A pdb=" N GLY D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 455 through 459 removed outlier: 3.597A pdb=" N ARG D 458 " --> pdb=" O GLY D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 474 Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 520 through 527 Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.890A pdb=" N LEU D 556 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN D 557 " --> pdb=" O SER D 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 553 through 557' Processing helix chain 'D' and resid 560 through 580 Processing helix chain 'D' and resid 634 through 665 removed outlier: 3.585A pdb=" N GLU D 665 " --> pdb=" O VAL D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 699 through 712 removed outlier: 4.043A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 717 removed outlier: 3.562A pdb=" N LEU D 717 " --> pdb=" O ARG D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 773 through 787 Processing helix chain 'D' and resid 790 through 801 removed outlier: 3.648A pdb=" N MET D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY D 801 " --> pdb=" O LYS D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 841 removed outlier: 5.219A pdb=" N GLY D 822 " --> pdb=" O GLN D 818 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE D 824 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU D 841 " --> pdb=" O VAL D 837 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 removed outlier: 3.848A pdb=" N ASP A 79 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA A 105 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ARG A 384 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER A 148 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.947A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.615A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 394 removed outlier: 6.659A pdb=" N LEU A 389 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR A 404 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 435 through 436 removed outlier: 6.371A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA7, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA8, first strand: chain 'A' and resid 736 through 738 Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 43 removed outlier: 6.215A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.431A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.297A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 392 through 395 Processing sheet with id=AB4, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB5, first strand: chain 'B' and resid 433 through 437 removed outlier: 7.043A pdb=" N LEU B 433 " --> pdb=" O GLU B 479 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ARG B 481 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL B 435 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB7, first strand: chain 'B' and resid 527 through 529 Processing sheet with id=AB8, first strand: chain 'B' and resid 735 through 738 Processing sheet with id=AB9, first strand: chain 'B' and resid 684 through 685 removed outlier: 5.963A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 83 removed outlier: 6.913A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N PHE C 107 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLY C 39 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU C 149 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N GLN C 131 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ARG C 384 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N SER C 148 " --> pdb=" O ARG C 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 198 through 199 removed outlier: 7.534A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 198 through 199 removed outlier: 6.744A pdb=" N THR C 171 " --> pdb=" O HIS C 225 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 227 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE C 256 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C 403 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER C 393 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS C 401 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.649A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 433 through 435 Processing sheet with id=AC6, first strand: chain 'C' and resid 444 through 446 Processing sheet with id=AC7, first strand: chain 'C' and resid 514 through 515 removed outlier: 4.186A pdb=" N ALA C 515 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY C 765 " --> pdb=" O ALA C 515 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 681 through 683 removed outlier: 6.754A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 74 through 83 removed outlier: 6.685A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR D 77 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N PHE D 107 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLY D 39 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.184A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE D 279 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER D 393 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS D 401 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS D 395 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 367 through 370 Processing sheet with id=AD3, first strand: chain 'D' and resid 478 through 482 removed outlier: 6.368A pdb=" N ILE D 434 " --> pdb=" O LEU D 512 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 444 through 445 removed outlier: 3.574A pdb=" N LEU D 445 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 534 through 536 Processing sheet with id=AD6, first strand: chain 'D' and resid 681 through 684 removed outlier: 6.466A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2994 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 2.68 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: 7563 1.34 - 1.46: 5736 1.46 - 1.58: 10757 1.58 - 1.70: 0 1.70 - 1.82: 220 Bond restraints: 24276 Sorted by residual: bond pdb=" C1 NAG B1003 " pdb=" O5 NAG B1003 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 NAG C1001 " pdb=" O5 NAG C1001 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG D1001 " pdb=" O5 NAG D1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.93e+00 bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 ... (remaining 24271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 32247 1.68 - 3.35: 503 3.35 - 5.03: 92 5.03 - 6.71: 17 6.71 - 8.38: 5 Bond angle restraints: 32864 Sorted by residual: angle pdb=" N ILE C 281 " pdb=" CA ILE C 281 " pdb=" C ILE C 281 " ideal model delta sigma weight residual 113.42 109.10 4.32 1.17e+00 7.31e-01 1.36e+01 angle pdb=" N VAL C 716 " pdb=" CA VAL C 716 " pdb=" C VAL C 716 " ideal model delta sigma weight residual 112.43 109.17 3.26 9.20e-01 1.18e+00 1.26e+01 angle pdb=" C GLN D 677 " pdb=" N THR D 678 " pdb=" CA THR D 678 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.92e+00 angle pdb=" CB MET C 340 " pdb=" CG MET C 340 " pdb=" SD MET C 340 " ideal model delta sigma weight residual 112.70 121.08 -8.38 3.00e+00 1.11e-01 7.81e+00 angle pdb=" C ILE B 64 " pdb=" N ASN B 65 " pdb=" CA ASN B 65 " ideal model delta sigma weight residual 121.94 116.46 5.48 2.00e+00 2.50e-01 7.52e+00 ... (remaining 32859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.24: 13548 23.24 - 46.47: 938 46.47 - 69.71: 82 69.71 - 92.94: 32 92.94 - 116.18: 27 Dihedral angle restraints: 14627 sinusoidal: 6006 harmonic: 8621 Sorted by residual: dihedral pdb=" CB CYS D 750 " pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " pdb=" CB CYS D 804 " ideal model delta sinusoidal sigma weight residual -86.00 -160.88 74.88 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CA PHE A 533 " pdb=" C PHE A 533 " pdb=" N MET A 534 " pdb=" CA MET A 534 " ideal model delta harmonic sigma weight residual 180.00 153.68 26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA MET A 737 " pdb=" C MET A 737 " pdb=" N GLU A 738 " pdb=" CA GLU A 738 " ideal model delta harmonic sigma weight residual -180.00 -156.86 -23.14 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 14624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3425 0.076 - 0.153: 299 0.153 - 0.229: 3 0.229 - 0.305: 1 0.305 - 0.382: 1 Chirality restraints: 3729 Sorted by residual: chirality pdb=" C1 NAG B1003 " pdb=" ND2 ASN B 751 " pdb=" C2 NAG B1003 " pdb=" O5 NAG B1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CB ILE B 820 " pdb=" CA ILE B 820 " pdb=" CG1 ILE B 820 " pdb=" CG2 ILE B 820 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C1 NAG A1002 " pdb=" ND2 ASN A 412 " pdb=" C2 NAG A1002 " pdb=" O5 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.62e-01 ... (remaining 3726 not shown) Planarity restraints: 4151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 306 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO A 307 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 564 " -0.011 2.00e-02 2.50e+03 1.18e-02 3.49e+00 pdb=" CG TRP C 564 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP C 564 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 564 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 564 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 564 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 564 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 564 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 564 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 564 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 79 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C ASP A 79 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP A 79 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 80 " 0.011 2.00e-02 2.50e+03 ... (remaining 4148 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2247 2.74 - 3.28: 24556 3.28 - 3.82: 40440 3.82 - 4.36: 46409 4.36 - 4.90: 80461 Nonbonded interactions: 194113 Sorted by model distance: nonbonded pdb=" OG SER C 560 " pdb=" OD1 ASP C 562 " model vdw 2.203 3.040 nonbonded pdb=" O MET B 247 " pdb=" OH TYR B 254 " model vdw 2.211 3.040 nonbonded pdb=" O PHE B 153 " pdb=" OG SER B 157 " model vdw 2.212 3.040 nonbonded pdb=" OE1 GLN B 119 " pdb=" NZ LYS B 135 " model vdw 2.217 3.120 nonbonded pdb=" OG1 THR A 208 " pdb=" OD1 ASP A 210 " model vdw 2.221 3.040 ... (remaining 194108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 580 or resid 633 through 663 or (resid 664 and \ (name N or name CA or name C or name O or name CB )) or resid 665 through 681 or \ (resid 682 and (name N or name CA or name C or name O or name CB )) or resid 68 \ 3 through 814 or (resid 815 and (name N or name CA or name C or name O or name C \ B )) or resid 816 through 1003)) selection = (chain 'B' and (resid 33 through 429 or resid 433 through 580 or resid 633 throu \ gh 681 or (resid 682 and (name N or name CA or name C or name O or name CB )) or \ resid 683 through 814 or (resid 815 and (name N or name CA or name C or name O \ or name CB )) or resid 816 through 834 or resid 1001 through 1003)) selection = (chain 'C' and (resid 33 through 428 or resid 434 through 580 or resid 633 throu \ gh 663 or (resid 664 and (name N or name CA or name C or name O or name CB )) or \ resid 665 through 834 or resid 1001 through 1003)) selection = (chain 'D' and (resid 33 through 681 or (resid 682 and (name N or name CA or nam \ e C or name O or name CB )) or resid 683 through 814 or (resid 815 and (name N o \ r name CA or name C or name O or name CB )) or resid 816 through 834 or resid 10 \ 01 through 1003)) } 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: 2.340 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.980 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.003 0.093 24293 Z= 0.135 Angle : 0.554 8.384 32910 Z= 0.276 Chirality : 0.041 0.382 3729 Planarity : 0.003 0.076 4139 Dihedral : 15.779 116.176 9068 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2954 helix: 1.46 (0.15), residues: 1263 sheet: -1.57 (0.29), residues: 361 loop : -1.56 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 358 TYR 0.015 0.001 TYR B 44 PHE 0.019 0.001 PHE D 642 TRP 0.032 0.001 TRP C 564 HIS 0.007 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00306 (24276) covalent geometry : angle 0.54749 (32864) SS BOND : bond 0.00521 ( 5) SS BOND : angle 0.97582 ( 10) hydrogen bonds : bond 0.15191 ( 1033) hydrogen bonds : angle 6.08974 ( 2994) link_NAG-ASN : bond 0.00535 ( 12) link_NAG-ASN : angle 2.51458 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 TYR cc_start: 0.3310 (m-10) cc_final: 0.2201 (m-80) REVERT: B 178 ASP cc_start: 0.7972 (m-30) cc_final: 0.7771 (m-30) REVERT: B 196 ASN cc_start: 0.6861 (t0) cc_final: 0.6586 (t0) REVERT: B 379 LYS cc_start: 0.7178 (mmtt) cc_final: 0.6881 (mmtt) REVERT: B 648 ILE cc_start: 0.9315 (tt) cc_final: 0.9083 (tt) REVERT: B 696 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7220 (pttm) REVERT: C 262 PHE cc_start: 0.7405 (p90) cc_final: 0.7187 (p90) REVERT: C 691 MET cc_start: 0.6458 (ptt) cc_final: 0.6221 (ptp) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1457 time to fit residues: 65.3135 Evaluate side-chains 224 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119300 restraints weight = 41857.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.118442 restraints weight = 100981.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.117326 restraints weight = 95610.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116407 restraints weight = 86838.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116490 restraints weight = 78181.422| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24293 Z= 0.218 Angle : 0.619 10.500 32910 Z= 0.311 Chirality : 0.045 0.302 3729 Planarity : 0.004 0.056 4139 Dihedral : 9.195 86.270 3465 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.97 % Allowed : 8.61 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.16), residues: 2954 helix: 1.32 (0.15), residues: 1269 sheet: -2.01 (0.26), residues: 391 loop : -1.55 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 713 TYR 0.024 0.002 TYR A 462 PHE 0.020 0.002 PHE B 107 TRP 0.013 0.001 TRP D 706 HIS 0.006 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00520 (24276) covalent geometry : angle 0.61408 (32864) SS BOND : bond 0.00316 ( 5) SS BOND : angle 0.58896 ( 10) hydrogen bonds : bond 0.04119 ( 1033) hydrogen bonds : angle 4.90139 ( 2994) link_NAG-ASN : bond 0.00535 ( 12) link_NAG-ASN : angle 2.42316 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.997 Fit side-chains REVERT: B 149 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8581 (mt) REVERT: B 196 ASN cc_start: 0.6860 (t0) cc_final: 0.6437 (t0) REVERT: B 379 LYS cc_start: 0.7334 (mmtt) cc_final: 0.7096 (mmtt) REVERT: B 696 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7355 (pttm) outliers start: 25 outliers final: 13 residues processed: 250 average time/residue: 0.1562 time to fit residues: 65.1960 Evaluate side-chains 238 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 224 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 737 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 51 optimal weight: 7.9990 chunk 109 optimal weight: 0.0980 chunk 85 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN B 714 GLN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS D 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.133188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.119819 restraints weight = 41640.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119279 restraints weight = 100352.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118869 restraints weight = 85940.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118226 restraints weight = 74086.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118409 restraints weight = 58149.662| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24293 Z= 0.115 Angle : 0.539 9.345 32910 Z= 0.268 Chirality : 0.041 0.241 3729 Planarity : 0.003 0.049 4139 Dihedral : 6.606 70.673 3465 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.97 % Allowed : 11.99 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.16), residues: 2954 helix: 1.44 (0.15), residues: 1288 sheet: -1.96 (0.27), residues: 383 loop : -1.53 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 748 TYR 0.026 0.001 TYR A 251 PHE 0.023 0.001 PHE C 658 TRP 0.012 0.001 TRP C 641 HIS 0.004 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00263 (24276) covalent geometry : angle 0.53381 (32864) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.50444 ( 10) hydrogen bonds : bond 0.03443 ( 1033) hydrogen bonds : angle 4.62043 ( 2994) link_NAG-ASN : bond 0.00410 ( 12) link_NAG-ASN : angle 2.38348 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 0.938 Fit side-chains REVERT: A 371 LEU cc_start: 0.8489 (tp) cc_final: 0.8235 (mp) REVERT: B 196 ASN cc_start: 0.6849 (t0) cc_final: 0.6414 (t0) REVERT: B 379 LYS cc_start: 0.7236 (mmtt) cc_final: 0.6974 (mmtt) REVERT: B 696 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7319 (pttm) outliers start: 25 outliers final: 13 residues processed: 260 average time/residue: 0.1569 time to fit residues: 67.3202 Evaluate side-chains 235 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 322 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 231 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 260 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 153 optimal weight: 0.3980 chunk 263 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115562 restraints weight = 41650.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115446 restraints weight = 102482.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114361 restraints weight = 71971.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113797 restraints weight = 74095.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114110 restraints weight = 50630.389| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24293 Z= 0.194 Angle : 0.571 9.364 32910 Z= 0.287 Chirality : 0.043 0.241 3729 Planarity : 0.004 0.046 4139 Dihedral : 5.670 70.558 3465 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.63 % Allowed : 14.62 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.16), residues: 2954 helix: 1.41 (0.15), residues: 1289 sheet: -2.07 (0.26), residues: 388 loop : -1.60 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 800 TYR 0.025 0.001 TYR A 78 PHE 0.022 0.001 PHE D 153 TRP 0.012 0.001 TRP D 368 HIS 0.004 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00466 (24276) covalent geometry : angle 0.56622 (32864) SS BOND : bond 0.00427 ( 5) SS BOND : angle 0.71283 ( 10) hydrogen bonds : bond 0.03572 ( 1033) hydrogen bonds : angle 4.58392 ( 2994) link_NAG-ASN : bond 0.00433 ( 12) link_NAG-ASN : angle 2.34236 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.949 Fit side-chains REVERT: B 149 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8479 (mt) REVERT: B 196 ASN cc_start: 0.6943 (t0) cc_final: 0.6458 (t0) REVERT: B 247 MET cc_start: 0.8461 (mtp) cc_final: 0.8164 (mtm) REVERT: B 413 MET cc_start: 0.8012 (ptm) cc_final: 0.7657 (ttp) REVERT: B 696 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7520 (pttm) REVERT: C 274 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7833 (m) outliers start: 42 outliers final: 21 residues processed: 259 average time/residue: 0.1467 time to fit residues: 63.5654 Evaluate side-chains 250 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 322 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 98 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 253 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 208 optimal weight: 0.3980 chunk 51 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.132743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.116945 restraints weight = 41193.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116704 restraints weight = 104028.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116257 restraints weight = 74874.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.115646 restraints weight = 73971.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115921 restraints weight = 50290.603| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24293 Z= 0.114 Angle : 0.519 9.377 32910 Z= 0.261 Chirality : 0.041 0.243 3729 Planarity : 0.003 0.044 4139 Dihedral : 5.194 68.869 3465 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.51 % Allowed : 15.71 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2954 helix: 1.52 (0.15), residues: 1293 sheet: -1.98 (0.26), residues: 395 loop : -1.53 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 300 TYR 0.023 0.001 TYR C 521 PHE 0.017 0.001 PHE A 555 TRP 0.014 0.001 TRP D 706 HIS 0.004 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00264 (24276) covalent geometry : angle 0.51359 (32864) SS BOND : bond 0.00143 ( 5) SS BOND : angle 0.56471 ( 10) hydrogen bonds : bond 0.03148 ( 1033) hydrogen bonds : angle 4.46199 ( 2994) link_NAG-ASN : bond 0.00396 ( 12) link_NAG-ASN : angle 2.22228 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 0.955 Fit side-chains REVERT: B 196 ASN cc_start: 0.6851 (t0) cc_final: 0.6398 (t0) REVERT: B 360 MET cc_start: 0.9082 (tpt) cc_final: 0.8483 (tpt) REVERT: B 413 MET cc_start: 0.7801 (ptm) cc_final: 0.7447 (ttt) REVERT: B 696 LYS cc_start: 0.7895 (mtmm) cc_final: 0.7432 (pttm) REVERT: B 735 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7423 (t80) REVERT: C 796 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6283 (tt0) outliers start: 39 outliers final: 22 residues processed: 266 average time/residue: 0.1585 time to fit residues: 70.0722 Evaluate side-chains 249 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 746 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 145 optimal weight: 8.9990 chunk 61 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 270 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118862 restraints weight = 41485.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118773 restraints weight = 105234.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118144 restraints weight = 84054.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117693 restraints weight = 73982.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117918 restraints weight = 52672.459| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24293 Z= 0.138 Angle : 0.531 9.349 32910 Z= 0.267 Chirality : 0.041 0.242 3729 Planarity : 0.003 0.044 4139 Dihedral : 5.020 67.277 3465 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.63 % Allowed : 16.49 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.16), residues: 2954 helix: 1.50 (0.15), residues: 1295 sheet: -1.97 (0.27), residues: 373 loop : -1.54 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 800 TYR 0.025 0.001 TYR D 44 PHE 0.026 0.001 PHE B 555 TRP 0.017 0.001 TRP D 706 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00326 (24276) covalent geometry : angle 0.52641 (32864) SS BOND : bond 0.00164 ( 5) SS BOND : angle 0.53965 ( 10) hydrogen bonds : bond 0.03206 ( 1033) hydrogen bonds : angle 4.43091 ( 2994) link_NAG-ASN : bond 0.00373 ( 12) link_NAG-ASN : angle 2.21946 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.955 Fit side-chains REVERT: A 41 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8587 (mm) REVERT: B 196 ASN cc_start: 0.6850 (t0) cc_final: 0.6386 (t0) REVERT: B 360 MET cc_start: 0.9150 (tpt) cc_final: 0.8623 (tpt) REVERT: B 413 MET cc_start: 0.7732 (ptm) cc_final: 0.7520 (ttp) REVERT: B 696 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7415 (pttm) REVERT: C 238 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8430 (mm) outliers start: 42 outliers final: 24 residues processed: 264 average time/residue: 0.1499 time to fit residues: 66.9606 Evaluate side-chains 251 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 746 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 158 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN D 784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.128862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112554 restraints weight = 41587.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112704 restraints weight = 112113.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112682 restraints weight = 87885.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112431 restraints weight = 62972.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112653 restraints weight = 51870.995| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 24293 Z= 0.279 Angle : 0.645 9.316 32910 Z= 0.327 Chirality : 0.045 0.327 3729 Planarity : 0.004 0.043 4139 Dihedral : 5.312 67.528 3465 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.94 % Allowed : 17.03 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.16), residues: 2954 helix: 1.18 (0.15), residues: 1281 sheet: -2.32 (0.25), residues: 392 loop : -1.63 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 713 TYR 0.025 0.002 TYR D 44 PHE 0.024 0.002 PHE D 153 TRP 0.019 0.002 TRP D 706 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00670 (24276) covalent geometry : angle 0.64046 (32864) SS BOND : bond 0.00328 ( 5) SS BOND : angle 0.78104 ( 10) hydrogen bonds : bond 0.03816 ( 1033) hydrogen bonds : angle 4.66992 ( 2994) link_NAG-ASN : bond 0.00437 ( 12) link_NAG-ASN : angle 2.46342 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 0.936 Fit side-chains REVERT: A 41 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8714 (mm) REVERT: A 153 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.6438 (m-80) REVERT: A 251 TYR cc_start: 0.4394 (m-10) cc_final: 0.3310 (m-80) REVERT: B 196 ASN cc_start: 0.6951 (t0) cc_final: 0.6455 (t0) REVERT: B 247 MET cc_start: 0.8456 (mtp) cc_final: 0.8170 (mtm) REVERT: B 696 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7613 (pttm) REVERT: D 563 ILE cc_start: 0.7672 (mm) cc_final: 0.7300 (mt) outliers start: 50 outliers final: 31 residues processed: 270 average time/residue: 0.1442 time to fit residues: 64.6715 Evaluate side-chains 261 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 746 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 76 optimal weight: 0.0470 chunk 289 optimal weight: 5.9990 chunk 44 optimal weight: 0.0020 chunk 21 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.5890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN B 819 ASN C 802 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116258 restraints weight = 41393.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115871 restraints weight = 99427.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115480 restraints weight = 80672.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114755 restraints weight = 69397.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114999 restraints weight = 57716.123| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 24293 Z= 0.118 Angle : 0.541 9.936 32910 Z= 0.273 Chirality : 0.041 0.276 3729 Planarity : 0.003 0.043 4139 Dihedral : 4.988 65.198 3465 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.28 % Allowed : 17.88 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.16), residues: 2954 helix: 1.37 (0.15), residues: 1295 sheet: -2.01 (0.27), residues: 377 loop : -1.54 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 800 TYR 0.026 0.001 TYR C 521 PHE 0.021 0.001 PHE B 555 TRP 0.021 0.001 TRP D 706 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00275 (24276) covalent geometry : angle 0.53652 (32864) SS BOND : bond 0.00156 ( 5) SS BOND : angle 0.57222 ( 10) hydrogen bonds : bond 0.03126 ( 1033) hydrogen bonds : angle 4.49017 ( 2994) link_NAG-ASN : bond 0.00393 ( 12) link_NAG-ASN : angle 2.20113 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.949 Fit side-chains REVERT: A 41 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8583 (mm) REVERT: A 251 TYR cc_start: 0.3631 (m-10) cc_final: 0.2707 (m-80) REVERT: B 196 ASN cc_start: 0.6864 (t0) cc_final: 0.6399 (t0) REVERT: B 696 LYS cc_start: 0.7962 (mtmm) cc_final: 0.7517 (pttm) REVERT: D 563 ILE cc_start: 0.7749 (mm) cc_final: 0.7397 (mt) outliers start: 33 outliers final: 24 residues processed: 253 average time/residue: 0.1366 time to fit residues: 57.6231 Evaluate side-chains 252 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 746 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 264 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 chunk 148 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 290 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115485 restraints weight = 41469.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115095 restraints weight = 103009.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114740 restraints weight = 82105.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.114132 restraints weight = 67455.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114433 restraints weight = 54782.866| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 24293 Z= 0.157 Angle : 0.561 9.582 32910 Z= 0.284 Chirality : 0.042 0.282 3729 Planarity : 0.003 0.043 4139 Dihedral : 4.913 64.014 3465 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.44 % Allowed : 18.00 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.16), residues: 2954 helix: 1.37 (0.15), residues: 1295 sheet: -2.01 (0.27), residues: 372 loop : -1.56 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 800 TYR 0.028 0.001 TYR C 521 PHE 0.022 0.001 PHE A 355 TRP 0.025 0.001 TRP D 706 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00379 (24276) covalent geometry : angle 0.55684 (32864) SS BOND : bond 0.00194 ( 5) SS BOND : angle 0.57795 ( 10) hydrogen bonds : bond 0.03272 ( 1033) hydrogen bonds : angle 4.48179 ( 2994) link_NAG-ASN : bond 0.00345 ( 12) link_NAG-ASN : angle 2.18665 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.916 Fit side-chains REVERT: A 41 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8649 (mm) REVERT: A 153 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: A 251 TYR cc_start: 0.3750 (m-10) cc_final: 0.2760 (m-80) REVERT: B 196 ASN cc_start: 0.6890 (t0) cc_final: 0.6424 (t0) REVERT: B 696 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7537 (pttm) REVERT: C 85 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6885 (mp) REVERT: C 234 MET cc_start: 0.7368 (tpp) cc_final: 0.6856 (tpp) REVERT: D 563 ILE cc_start: 0.7590 (mm) cc_final: 0.7241 (mt) outliers start: 37 outliers final: 27 residues processed: 254 average time/residue: 0.1394 time to fit residues: 59.9769 Evaluate side-chains 252 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 746 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 84 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 272 optimal weight: 0.0670 chunk 144 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116715 restraints weight = 41396.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116180 restraints weight = 101338.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115792 restraints weight = 81670.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115071 restraints weight = 69016.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115385 restraints weight = 55254.587| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24293 Z= 0.118 Angle : 0.541 12.362 32910 Z= 0.273 Chirality : 0.041 0.277 3729 Planarity : 0.003 0.043 4139 Dihedral : 4.798 62.427 3465 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.32 % Allowed : 18.04 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2954 helix: 1.42 (0.15), residues: 1295 sheet: -2.01 (0.28), residues: 360 loop : -1.51 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 800 TYR 0.028 0.001 TYR C 521 PHE 0.023 0.001 PHE A 355 TRP 0.026 0.001 TRP D 706 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00277 (24276) covalent geometry : angle 0.53647 (32864) SS BOND : bond 0.00147 ( 5) SS BOND : angle 0.49680 ( 10) hydrogen bonds : bond 0.03083 ( 1033) hydrogen bonds : angle 4.43130 ( 2994) link_NAG-ASN : bond 0.00357 ( 12) link_NAG-ASN : angle 2.10017 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.954 Fit side-chains REVERT: A 41 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8580 (mm) REVERT: A 153 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: A 251 TYR cc_start: 0.3400 (m-10) cc_final: 0.2435 (m-80) REVERT: B 196 ASN cc_start: 0.6847 (t0) cc_final: 0.6384 (t0) REVERT: B 696 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7469 (pttm) REVERT: C 85 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6767 (mp) REVERT: D 413 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7668 (mtm) REVERT: D 563 ILE cc_start: 0.7653 (mm) cc_final: 0.7312 (mt) outliers start: 34 outliers final: 29 residues processed: 253 average time/residue: 0.1440 time to fit residues: 60.2782 Evaluate side-chains 256 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 746 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 196 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 179 optimal weight: 0.0970 chunk 37 optimal weight: 6.9990 chunk 240 optimal weight: 0.7980 chunk 145 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116516 restraints weight = 41202.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116109 restraints weight = 98878.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115655 restraints weight = 78711.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.115038 restraints weight = 69168.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115282 restraints weight = 54791.837| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24293 Z= 0.131 Angle : 0.544 10.730 32910 Z= 0.275 Chirality : 0.041 0.274 3729 Planarity : 0.003 0.043 4139 Dihedral : 4.753 61.135 3465 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.51 % Allowed : 18.23 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.16), residues: 2954 helix: 1.44 (0.15), residues: 1293 sheet: -2.10 (0.27), residues: 372 loop : -1.51 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 800 TYR 0.026 0.001 TYR C 521 PHE 0.026 0.001 PHE C 744 TRP 0.026 0.001 TRP D 706 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00311 (24276) covalent geometry : angle 0.54010 (32864) SS BOND : bond 0.00169 ( 5) SS BOND : angle 0.49412 ( 10) hydrogen bonds : bond 0.03121 ( 1033) hydrogen bonds : angle 4.41585 ( 2994) link_NAG-ASN : bond 0.00341 ( 12) link_NAG-ASN : angle 2.13393 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2930.31 seconds wall clock time: 52 minutes 20.48 seconds (3140.48 seconds total)