Starting phenix.real_space_refine on Sun May 18 22:24:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szg_40915/05_2025/8szg_40915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szg_40915/05_2025/8szg_40915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8szg_40915/05_2025/8szg_40915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szg_40915/05_2025/8szg_40915.map" model { file = "/net/cci-nas-00/data/ceres_data/8szg_40915/05_2025/8szg_40915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szg_40915/05_2025/8szg_40915.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.048 sd= 0.126 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 3 5.49 5 S 100 5.16 5 C 11359 2.51 5 N 2904 2.21 5 O 3196 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17571 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2404 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 142 Chain: "E" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 368 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 6520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6520 Classifications: {'peptide': 830} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 32, 'TRANS': 797} Chain breaks: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "B" Number of atoms: 6279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6279 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 31, 'TRANS': 764} Chain breaks: 3 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1640 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 130 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 159 Unusual residues: {' CA': 3, 'NAG': 2, 'PCW': 1, 'PO4': 1, 'SPM': 2, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1208 "'] Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 117 Unusual residues: {'CLR': 1, 'NAG': 2, 'PO4': 1, 'SPM': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1405 "'] Classifications: {'peptide': 1, 'undetermined': 6, 'water': 1} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.70, per 1000 atoms: 0.55 Number of scatterers: 17571 At special positions: 0 Unit cell: (102.389, 108.463, 251.633, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 100 16.00 P 3 15.00 F 6 9.00 O 3196 8.00 N 2904 7.00 C 11359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1202 " - " ASN A 287 " " NAG A1203 " - " ASN A 468 " " NAG B1402 " - " ASN B 468 " " NAG B1403 " - " ASN B 488 " " NAG F 1 " - " ASN A 488 " " NAG G 1 " - " ASN A 541 " " NAG H 1 " - " ASN B 541 " Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 2.1 seconds 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4216 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 24 sheets defined 43.5% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'D' and resid 6 through 26 removed outlier: 3.703A pdb=" N ALA D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 10 through 24 removed outlier: 3.647A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.626A pdb=" N HIS E 44 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.757A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.614A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.929A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.749A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.659A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.513A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.978A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 4.458A pdb=" N HIS A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.831A pdb=" N PHE A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.758A pdb=" N SER A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 404 " --> pdb=" O ILE A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.193A pdb=" N VAL A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.522A pdb=" N VAL A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.862A pdb=" N LEU A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.561A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 4.039A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 673 through 706 removed outlier: 5.064A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix Processing helix chain 'A' and resid 716 through 746 removed outlier: 3.606A pdb=" N LEU A 723 " --> pdb=" O TRP A 719 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 729 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 794 removed outlier: 3.515A pdb=" N GLY A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 821 removed outlier: 3.565A pdb=" N LEU A 812 " --> pdb=" O THR A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 removed outlier: 3.550A pdb=" N TYR A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 863 removed outlier: 3.844A pdb=" N PHE A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 867 Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.886A pdb=" N VAL A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.562A pdb=" N PHE B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.596A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.885A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.699A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.543A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.912A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 262 removed outlier: 3.524A pdb=" N SER B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.568A pdb=" N PHE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 416 through 436 removed outlier: 3.544A pdb=" N VAL B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.547A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 removed outlier: 3.557A pdb=" N ILE B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.855A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 666 removed outlier: 3.579A pdb=" N PHE B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 669 No H-bonds generated for 'chain 'B' and resid 667 through 669' Processing helix chain 'B' and resid 673 through 698 removed outlier: 3.647A pdb=" N CYS B 677 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLN B 681 " --> pdb=" O CYS B 677 " (cutoff:3.500A) Proline residue: B 682 - end of helix removed outlier: 3.512A pdb=" N ILE B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 706 removed outlier: 4.514A pdb=" N PHE B 706 " --> pdb=" O VAL B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.774A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 794 removed outlier: 3.688A pdb=" N ALA B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 826 removed outlier: 3.901A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 832 through 862 removed outlier: 3.606A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 36 Processing helix chain 'C' and resid 51 through 62 removed outlier: 3.539A pdb=" N GLN C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 233 through 236 removed outlier: 4.000A pdb=" N ASP C 236 " --> pdb=" O SER C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 246 through 261 removed outlier: 3.753A pdb=" N GLU C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 261 " --> pdb=" O THR C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 282 removed outlier: 4.004A pdb=" N LEU C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 removed outlier: 4.577A pdb=" N TYR C 291 " --> pdb=" O HIS C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 316 removed outlier: 3.767A pdb=" N LEU C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 356 Processing sheet with id=AA1, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.351A pdb=" N THR D 47 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN D 340 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 337 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.945A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 73 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 72 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 80 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 104 through 105 removed outlier: 3.590A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 148 through 151 removed outlier: 3.804A pdb=" N CYS D 148 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.660A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 201 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 209 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.751A pdb=" N ALA D 231 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 253 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 251 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 252 " --> pdb=" O MET D 262 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 273 through 278 removed outlier: 4.194A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL D 296 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.493A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 142 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 236 through 243 removed outlier: 8.194A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 269 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.872A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 470 removed outlier: 3.636A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB4, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AB5, first strand: chain 'A' and resid 589 through 590 Processing sheet with id=AB6, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.189A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N CYS A 765 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.635A pdb=" N TYR B 95 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 142 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.051A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AC1, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC2, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AC3, first strand: chain 'B' and resid 602 through 604 removed outlier: 6.614A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 749 through 750 removed outlier: 3.786A pdb=" N SER B 749 " --> pdb=" O HIS B 766 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.648A pdb=" N LEU C 40 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 225 through 231 removed outlier: 5.970A pdb=" N ILE C 226 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE C 272 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE C 228 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASN C 274 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 230 " --> pdb=" O ASN C 274 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.40 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2955 1.32 - 1.46: 5579 1.46 - 1.59: 9309 1.59 - 1.72: 6 1.72 - 1.86: 127 Bond restraints: 17976 Sorted by residual: bond pdb=" C31 PCW A1204 " pdb=" O2 PCW A1204 " ideal model delta sigma weight residual 1.333 1.487 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" CG1 ILE C 337 " pdb=" CD1 ILE C 337 " ideal model delta sigma weight residual 1.513 1.267 0.246 3.90e-02 6.57e+02 3.96e+01 bond pdb=" C16 PCW A1204 " pdb=" C17 PCW A1204 " ideal model delta sigma weight residual 1.523 1.623 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C31 PCW A1204 " pdb=" C32 PCW A1204 " ideal model delta sigma weight residual 1.502 1.601 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C11 PCW A1204 " pdb=" O3 PCW A1204 " ideal model delta sigma weight residual 1.326 1.417 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 17971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 24318 4.95 - 9.90: 75 9.90 - 14.84: 5 14.84 - 19.79: 1 19.79 - 24.74: 2 Bond angle restraints: 24401 Sorted by residual: angle pdb=" C PHE C 341 " pdb=" CA PHE C 341 " pdb=" CB PHE C 341 " ideal model delta sigma weight residual 110.85 88.88 21.97 1.70e+00 3.46e-01 1.67e+02 angle pdb=" C18 PCW A1204 " pdb=" C19 PCW A1204 " pdb=" C20 PCW A1204 " ideal model delta sigma weight residual 127.82 152.56 -24.74 3.00e+00 1.11e-01 6.80e+01 angle pdb=" C THR B 596 " pdb=" CA THR B 596 " pdb=" CB THR B 596 " ideal model delta sigma weight residual 110.88 98.18 12.70 1.57e+00 4.06e-01 6.54e+01 angle pdb=" N LYS C 345 " pdb=" CA LYS C 345 " pdb=" C LYS C 345 " ideal model delta sigma weight residual 111.07 103.21 7.86 1.07e+00 8.73e-01 5.40e+01 angle pdb=" N ILE B 434 " pdb=" CA ILE B 434 " pdb=" C ILE B 434 " ideal model delta sigma weight residual 110.72 103.40 7.32 1.01e+00 9.80e-01 5.25e+01 ... (remaining 24396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 10481 32.59 - 65.17: 266 65.17 - 97.76: 25 97.76 - 130.34: 1 130.34 - 162.93: 1 Dihedral angle restraints: 10774 sinusoidal: 4269 harmonic: 6505 Sorted by residual: dihedral pdb=" C PHE C 341 " pdb=" N PHE C 341 " pdb=" CA PHE C 341 " pdb=" CB PHE C 341 " ideal model delta harmonic sigma weight residual -122.60 -95.83 -26.77 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual -86.00 -176.09 90.09 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS B 585 " pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " pdb=" CB CYS B 598 " ideal model delta sinusoidal sigma weight residual -86.00 -169.45 83.45 1 1.00e+01 1.00e-02 8.50e+01 ... (remaining 10771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.027: 2785 1.027 - 2.053: 0 2.053 - 3.080: 0 3.080 - 4.107: 0 4.107 - 5.133: 1 Chirality restraints: 2786 Sorted by residual: chirality pdb=" C2 PCW A1204 " pdb=" C1 PCW A1204 " pdb=" C3 PCW A1204 " pdb=" O2 PCW A1204 " both_signs ideal model delta sigma weight residual False -2.32 2.81 -5.13 2.00e-01 2.50e+01 6.59e+02 chirality pdb=" CA ASP C 346 " pdb=" N ASP C 346 " pdb=" C ASP C 346 " pdb=" CB ASP C 346 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.48e+01 ... (remaining 2783 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 821 " -0.044 2.00e-02 2.50e+03 4.41e-02 3.40e+01 pdb=" CG PHE B 821 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE B 821 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 PHE B 821 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE B 821 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE B 821 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 821 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 792 " 0.030 2.00e-02 2.50e+03 3.97e-02 2.75e+01 pdb=" CG PHE B 792 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 792 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 PHE B 792 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE B 792 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 PHE B 792 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 792 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 712 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C THR A 712 " -0.073 2.00e-02 2.50e+03 pdb=" O THR A 712 " 0.028 2.00e-02 2.50e+03 pdb=" N SER A 713 " 0.024 2.00e-02 2.50e+03 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4758 2.80 - 3.33: 15600 3.33 - 3.85: 26727 3.85 - 4.38: 30397 4.38 - 4.90: 53679 Nonbonded interactions: 131161 Sorted by model distance: nonbonded pdb=" OG1 THR B 550 " pdb=" O VAL B 566 " model vdw 2.281 3.040 nonbonded pdb=" O SER D 31 " pdb=" OG SER D 31 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR D 102 " pdb=" O SER D 147 " model vdw 2.308 3.040 nonbonded pdb=" OE1 GLU B 229 " pdb=" NH1 ARG B 233 " model vdw 2.308 3.120 nonbonded pdb=" NH2 ARG B 69 " pdb=" O2 PO4 B1406 " model vdw 2.326 3.120 ... (remaining 131156 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 20 through 118 or (resid 119 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 362 or resid 392 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 through 516 or (resid 517 and (name N or name CA or name C or name \ O or name CB )) or resid 518 through 546 or (resid 547 through 548 and (name N \ or name CA or name C or name O or name CB )) or resid 549 through 586 or (resid \ 587 through 588 and (name N or name CA or name C or name O or name CB )) or resi \ d 589 through 673 or (resid 674 and (name N or name CA or name C or name O or na \ me CB )) or resid 675 through 707 or resid 722 through 734 or (resid 735 and (na \ me N or name CA or name C or name O or name CB )) or resid 736 through 756 or (r \ esid 757 and (name N or name CA or name C or name O or name CB )) or resid 758 t \ hrough 801 or (resid 802 and (name N or name CA or name C or name O or name CB ) \ ) or resid 803 through 868 or (resid 869 through 871 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1208 through 1209)) selection = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 120 or (resid 134 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 through 360 or \ (resid 361 through 362 and (name N or name CA or name C or name O or name CB )) \ or resid 392 through 480 or (resid 481 and (name N or name CA or name C or name \ O or name CB )) or resid 482 through 498 or (resid 499 through 500 and (name N \ or name CA or name C or name O or name CB )) or resid 501 through 591 or (resid \ 592 through 593 and (name N or name CA or name C or name O or name CB )) or resi \ d 594 through 608 or (resid 609 through 610 and (name N or name CA or name C or \ name O or name CB )) or resid 611 through 670 or (resid 671 and (name N or name \ CA or name C or name O or name CB )) or resid 672 through 706 or (resid 707 thro \ ugh 722 and (name N or name CA or name C or name O or name CB )) or resid 723 th \ rough 871 or resid 1405 through 1406)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 19.830 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 39.260 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.006 0.246 18004 Z= 0.343 Angle : 0.853 24.740 24467 Z= 0.519 Chirality : 0.114 5.133 2786 Planarity : 0.005 0.050 3061 Dihedral : 14.080 162.926 6504 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2209 helix: 0.79 (0.18), residues: 869 sheet: -0.76 (0.29), residues: 347 loop : -1.25 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 742 HIS 0.010 0.001 HIS A 879 PHE 0.085 0.003 PHE B 821 TYR 0.031 0.002 TYR B 829 ARG 0.018 0.000 ARG A 701 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 7) link_NAG-ASN : angle 1.50539 ( 21) link_BETA1-4 : bond 0.00536 ( 3) link_BETA1-4 : angle 1.21680 ( 9) hydrogen bonds : bond 0.19316 ( 732) hydrogen bonds : angle 6.38958 ( 2106) SS BOND : bond 0.00241 ( 18) SS BOND : angle 1.60138 ( 36) covalent geometry : bond 0.00632 (17976) covalent geometry : angle 0.85083 (24401) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8753 (mppt) cc_final: 0.8405 (mmtm) REVERT: D 63 TRP cc_start: 0.7781 (m100) cc_final: 0.7371 (m100) REVERT: A 790 PHE cc_start: 0.8329 (m-10) cc_final: 0.7984 (m-80) REVERT: A 832 PHE cc_start: 0.6995 (m-10) cc_final: 0.6712 (m-80) REVERT: B 510 TYR cc_start: 0.8072 (p90) cc_final: 0.7869 (p90) REVERT: B 558 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 618 LEU cc_start: 0.7929 (mt) cc_final: 0.7534 (pp) REVERT: B 738 ILE cc_start: 0.7575 (tp) cc_final: 0.7296 (tt) REVERT: C 29 LEU cc_start: 0.8964 (tp) cc_final: 0.8689 (tt) REVERT: C 44 LEU cc_start: 0.7931 (tp) cc_final: 0.7509 (tp) REVERT: C 259 ILE cc_start: 0.8241 (mm) cc_final: 0.7756 (tt) REVERT: C 282 LYS cc_start: 0.7408 (mtpt) cc_final: 0.7189 (mtpp) outliers start: 2 outliers final: 1 residues processed: 303 average time/residue: 0.3040 time to fit residues: 138.0036 Evaluate side-chains 240 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 173 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 200 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 471 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.088631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.072583 restraints weight = 49509.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072789 restraints weight = 40126.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073287 restraints weight = 38925.032| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18004 Z= 0.123 Angle : 0.557 9.263 24467 Z= 0.294 Chirality : 0.043 0.252 2786 Planarity : 0.004 0.043 3061 Dihedral : 8.724 84.207 2762 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.01 % Allowed : 8.61 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2209 helix: 1.40 (0.18), residues: 877 sheet: -0.59 (0.28), residues: 367 loop : -1.31 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 818 HIS 0.008 0.001 HIS B 359 PHE 0.019 0.001 PHE A 814 TYR 0.020 0.001 TYR D 111 ARG 0.007 0.000 ARG E 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 7) link_NAG-ASN : angle 1.31496 ( 21) link_BETA1-4 : bond 0.00434 ( 3) link_BETA1-4 : angle 1.05273 ( 9) hydrogen bonds : bond 0.05561 ( 732) hydrogen bonds : angle 4.54501 ( 2106) SS BOND : bond 0.00259 ( 18) SS BOND : angle 2.11236 ( 36) covalent geometry : bond 0.00256 (17976) covalent geometry : angle 0.55002 (24401) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8659 (mppt) cc_final: 0.8413 (mmtm) REVERT: D 63 TRP cc_start: 0.7674 (m100) cc_final: 0.7323 (m100) REVERT: A 760 ILE cc_start: 0.8657 (mt) cc_final: 0.8326 (mm) REVERT: A 789 PHE cc_start: 0.8531 (t80) cc_final: 0.8215 (t80) REVERT: A 790 PHE cc_start: 0.8013 (m-10) cc_final: 0.7657 (m-80) REVERT: A 829 TYR cc_start: 0.7988 (p90) cc_final: 0.7633 (p90) REVERT: A 832 PHE cc_start: 0.6999 (m-10) cc_final: 0.6711 (m-80) REVERT: B 446 ASN cc_start: 0.7747 (t0) cc_final: 0.7514 (t0) REVERT: B 558 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 852 ILE cc_start: 0.8477 (mt) cc_final: 0.8248 (mm) REVERT: C 29 LEU cc_start: 0.8805 (tp) cc_final: 0.8538 (tt) REVERT: C 252 LYS cc_start: 0.7304 (mtpp) cc_final: 0.7003 (mtpp) REVERT: C 259 ILE cc_start: 0.8122 (mm) cc_final: 0.7468 (pt) REVERT: C 316 LEU cc_start: 0.8001 (tt) cc_final: 0.7699 (mt) REVERT: C 321 ASP cc_start: 0.7050 (t0) cc_final: 0.6797 (t0) outliers start: 18 outliers final: 9 residues processed: 258 average time/residue: 0.3104 time to fit residues: 120.2913 Evaluate side-chains 240 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 231 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 815 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 26 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 800 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.086542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070242 restraints weight = 49498.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.070238 restraints weight = 43644.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070837 restraints weight = 39020.028| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18004 Z= 0.195 Angle : 0.591 12.161 24467 Z= 0.311 Chirality : 0.045 0.236 2786 Planarity : 0.004 0.047 3061 Dihedral : 8.404 79.980 2761 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.25 % Rotamer: Outliers : 1.57 % Allowed : 11.29 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2209 helix: 1.28 (0.18), residues: 881 sheet: -0.82 (0.28), residues: 365 loop : -1.38 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 530 HIS 0.007 0.001 HIS B 359 PHE 0.018 0.002 PHE A 814 TYR 0.016 0.002 TYR B 425 ARG 0.007 0.000 ARG B 551 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 7) link_NAG-ASN : angle 1.72344 ( 21) link_BETA1-4 : bond 0.00355 ( 3) link_BETA1-4 : angle 1.35416 ( 9) hydrogen bonds : bond 0.06014 ( 732) hydrogen bonds : angle 4.36874 ( 2106) SS BOND : bond 0.00243 ( 18) SS BOND : angle 1.88788 ( 36) covalent geometry : bond 0.00463 (17976) covalent geometry : angle 0.58433 (24401) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7764 (m100) cc_final: 0.7368 (m100) REVERT: D 234 PHE cc_start: 0.5248 (t80) cc_final: 0.4880 (t80) REVERT: A 760 ILE cc_start: 0.8659 (mt) cc_final: 0.8344 (mm) REVERT: A 790 PHE cc_start: 0.8150 (m-10) cc_final: 0.7748 (m-80) REVERT: A 829 TYR cc_start: 0.8025 (p90) cc_final: 0.7757 (p90) REVERT: A 832 PHE cc_start: 0.7053 (m-10) cc_final: 0.6781 (m-80) REVERT: B 446 ASN cc_start: 0.7802 (t0) cc_final: 0.7447 (t0) REVERT: B 558 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7769 (mm-30) REVERT: B 738 ILE cc_start: 0.7457 (tp) cc_final: 0.7158 (tt) REVERT: C 27 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7311 (ptp-170) REVERT: C 29 LEU cc_start: 0.8826 (tp) cc_final: 0.8569 (tt) REVERT: C 252 LYS cc_start: 0.7327 (mtpp) cc_final: 0.6928 (mtmm) REVERT: C 259 ILE cc_start: 0.8165 (mm) cc_final: 0.7495 (pt) REVERT: C 312 MET cc_start: 0.8238 (tpp) cc_final: 0.7964 (tmm) REVERT: C 321 ASP cc_start: 0.7118 (t0) cc_final: 0.6891 (t0) outliers start: 28 outliers final: 20 residues processed: 252 average time/residue: 0.3045 time to fit residues: 115.1557 Evaluate side-chains 245 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS A 253 GLN B 359 HIS B 471 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.087787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071689 restraints weight = 49804.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.071576 restraints weight = 45681.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072294 restraints weight = 38486.439| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18004 Z= 0.118 Angle : 0.515 10.239 24467 Z= 0.270 Chirality : 0.042 0.232 2786 Planarity : 0.004 0.044 3061 Dihedral : 7.846 77.797 2761 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.40 % Allowed : 12.97 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2209 helix: 1.49 (0.18), residues: 877 sheet: -0.69 (0.28), residues: 355 loop : -1.35 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 263 HIS 0.004 0.001 HIS B 359 PHE 0.019 0.001 PHE B 789 TYR 0.014 0.001 TYR E 40 ARG 0.004 0.000 ARG E 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 7) link_NAG-ASN : angle 1.47296 ( 21) link_BETA1-4 : bond 0.00373 ( 3) link_BETA1-4 : angle 1.10006 ( 9) hydrogen bonds : bond 0.04778 ( 732) hydrogen bonds : angle 4.09736 ( 2106) SS BOND : bond 0.00345 ( 18) SS BOND : angle 1.09701 ( 36) covalent geometry : bond 0.00261 (17976) covalent geometry : angle 0.51134 (24401) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7748 (m100) cc_final: 0.7398 (m100) REVERT: D 234 PHE cc_start: 0.5242 (t80) cc_final: 0.4954 (t80) REVERT: D 334 SER cc_start: 0.6564 (p) cc_final: 0.6153 (p) REVERT: A 760 ILE cc_start: 0.8671 (mt) cc_final: 0.8310 (mm) REVERT: A 790 PHE cc_start: 0.8085 (m-10) cc_final: 0.7753 (m-10) REVERT: A 829 TYR cc_start: 0.7975 (p90) cc_final: 0.7724 (p90) REVERT: A 832 PHE cc_start: 0.7009 (m-10) cc_final: 0.6750 (m-80) REVERT: B 446 ASN cc_start: 0.7781 (t0) cc_final: 0.7379 (t0) REVERT: B 558 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 738 ILE cc_start: 0.7532 (tp) cc_final: 0.7244 (tt) REVERT: C 27 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7303 (ptp-170) REVERT: C 29 LEU cc_start: 0.8811 (tp) cc_final: 0.8552 (tt) REVERT: C 259 ILE cc_start: 0.8110 (mm) cc_final: 0.7437 (pt) outliers start: 25 outliers final: 18 residues processed: 250 average time/residue: 0.3170 time to fit residues: 119.0699 Evaluate side-chains 242 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 28 optimal weight: 8.9990 chunk 175 optimal weight: 0.8980 chunk 151 optimal weight: 0.0670 chunk 2 optimal weight: 0.4980 chunk 12 optimal weight: 0.0870 chunk 141 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 218 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.088511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072311 restraints weight = 50248.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.072318 restraints weight = 43167.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.073008 restraints weight = 36877.126| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18004 Z= 0.103 Angle : 0.499 14.012 24467 Z= 0.258 Chirality : 0.041 0.228 2786 Planarity : 0.003 0.045 3061 Dihedral : 7.179 76.903 2761 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.62 % Allowed : 13.47 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.18), residues: 2209 helix: 1.60 (0.18), residues: 878 sheet: -0.68 (0.28), residues: 371 loop : -1.30 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 169 HIS 0.005 0.001 HIS B 359 PHE 0.019 0.001 PHE B 789 TYR 0.013 0.001 TYR B 751 ARG 0.004 0.000 ARG D 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 7) link_NAG-ASN : angle 1.32447 ( 21) link_BETA1-4 : bond 0.00314 ( 3) link_BETA1-4 : angle 1.06936 ( 9) hydrogen bonds : bond 0.04139 ( 732) hydrogen bonds : angle 3.95145 ( 2106) SS BOND : bond 0.00140 ( 18) SS BOND : angle 1.27058 ( 36) covalent geometry : bond 0.00224 (17976) covalent geometry : angle 0.49538 (24401) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7758 (m100) cc_final: 0.7423 (m100) REVERT: D 234 PHE cc_start: 0.5358 (t80) cc_final: 0.5091 (t80) REVERT: D 334 SER cc_start: 0.6506 (p) cc_final: 0.6089 (p) REVERT: A 760 ILE cc_start: 0.8662 (mt) cc_final: 0.8367 (mm) REVERT: A 790 PHE cc_start: 0.8060 (m-10) cc_final: 0.7659 (m-80) REVERT: A 829 TYR cc_start: 0.7940 (p90) cc_final: 0.7689 (p90) REVERT: A 832 PHE cc_start: 0.6946 (m-10) cc_final: 0.6724 (m-80) REVERT: B 446 ASN cc_start: 0.7759 (t0) cc_final: 0.7342 (t0) REVERT: B 558 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7684 (mm-30) REVERT: B 738 ILE cc_start: 0.7537 (tp) cc_final: 0.7321 (tt) REVERT: C 29 LEU cc_start: 0.8825 (tp) cc_final: 0.8556 (tt) REVERT: C 212 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6879 (mm-30) REVERT: C 259 ILE cc_start: 0.8069 (mm) cc_final: 0.7402 (pt) REVERT: C 321 ASP cc_start: 0.6667 (t0) cc_final: 0.6386 (t0) REVERT: C 322 LYS cc_start: 0.6526 (ptmm) cc_final: 0.6111 (pttp) outliers start: 29 outliers final: 23 residues processed: 251 average time/residue: 0.3099 time to fit residues: 118.7847 Evaluate side-chains 243 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 218 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 84 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 chunk 201 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN B 359 HIS C 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.087540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.071261 restraints weight = 49884.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.071140 restraints weight = 43519.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071711 restraints weight = 40165.851| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18004 Z= 0.125 Angle : 0.514 11.932 24467 Z= 0.268 Chirality : 0.042 0.231 2786 Planarity : 0.003 0.045 3061 Dihedral : 7.046 75.978 2761 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.07 % Allowed : 13.64 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2209 helix: 1.63 (0.18), residues: 878 sheet: -0.62 (0.28), residues: 355 loop : -1.31 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 530 HIS 0.013 0.001 HIS C 218 PHE 0.024 0.001 PHE B 789 TYR 0.015 0.001 TYR B 751 ARG 0.004 0.000 ARG A 866 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 7) link_NAG-ASN : angle 1.41816 ( 21) link_BETA1-4 : bond 0.00318 ( 3) link_BETA1-4 : angle 1.11911 ( 9) hydrogen bonds : bond 0.04425 ( 732) hydrogen bonds : angle 3.93664 ( 2106) SS BOND : bond 0.00162 ( 18) SS BOND : angle 1.42479 ( 36) covalent geometry : bond 0.00290 (17976) covalent geometry : angle 0.50941 (24401) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7750 (m100) cc_final: 0.7374 (m100) REVERT: D 234 PHE cc_start: 0.5330 (t80) cc_final: 0.5077 (t80) REVERT: D 334 SER cc_start: 0.6524 (p) cc_final: 0.6104 (p) REVERT: A 719 TRP cc_start: 0.6887 (t60) cc_final: 0.6259 (t-100) REVERT: A 760 ILE cc_start: 0.8651 (mt) cc_final: 0.8347 (mm) REVERT: A 790 PHE cc_start: 0.8123 (m-10) cc_final: 0.7767 (m-80) REVERT: A 832 PHE cc_start: 0.6988 (m-10) cc_final: 0.6748 (m-80) REVERT: B 446 ASN cc_start: 0.7788 (t0) cc_final: 0.7363 (t0) REVERT: B 558 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7713 (mm-30) REVERT: C 29 LEU cc_start: 0.8819 (tp) cc_final: 0.8561 (tt) REVERT: C 212 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7103 (mm-30) REVERT: C 259 ILE cc_start: 0.8027 (mm) cc_final: 0.7362 (pt) REVERT: C 321 ASP cc_start: 0.6851 (t0) cc_final: 0.6607 (t0) outliers start: 37 outliers final: 25 residues processed: 247 average time/residue: 0.3000 time to fit residues: 112.3954 Evaluate side-chains 249 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 13 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 47 optimal weight: 0.0770 chunk 145 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.087337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.071063 restraints weight = 49717.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070993 restraints weight = 43378.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071677 restraints weight = 37038.957| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18004 Z= 0.130 Angle : 0.526 11.264 24467 Z= 0.274 Chirality : 0.042 0.230 2786 Planarity : 0.004 0.045 3061 Dihedral : 6.888 74.559 2761 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.96 % Allowed : 14.14 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2209 helix: 1.61 (0.18), residues: 880 sheet: -0.62 (0.28), residues: 355 loop : -1.31 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 530 HIS 0.004 0.001 HIS C 218 PHE 0.034 0.001 PHE B 789 TYR 0.013 0.001 TYR B 751 ARG 0.004 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 7) link_NAG-ASN : angle 1.47169 ( 21) link_BETA1-4 : bond 0.00268 ( 3) link_BETA1-4 : angle 1.12882 ( 9) hydrogen bonds : bond 0.04539 ( 732) hydrogen bonds : angle 3.93548 ( 2106) SS BOND : bond 0.00356 ( 18) SS BOND : angle 1.57210 ( 36) covalent geometry : bond 0.00303 (17976) covalent geometry : angle 0.52052 (24401) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7753 (m100) cc_final: 0.7405 (m100) REVERT: D 334 SER cc_start: 0.6523 (p) cc_final: 0.6096 (p) REVERT: E 21 MET cc_start: 0.7230 (ppp) cc_final: 0.6267 (ttp) REVERT: A 719 TRP cc_start: 0.6879 (t60) cc_final: 0.6259 (t-100) REVERT: A 760 ILE cc_start: 0.8656 (mt) cc_final: 0.8377 (mm) REVERT: A 790 PHE cc_start: 0.8139 (m-10) cc_final: 0.7780 (m-80) REVERT: A 832 PHE cc_start: 0.6962 (m-10) cc_final: 0.6695 (m-80) REVERT: B 446 ASN cc_start: 0.7767 (t0) cc_final: 0.7334 (t0) REVERT: B 558 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7712 (mm-30) REVERT: C 29 LEU cc_start: 0.8819 (tp) cc_final: 0.8592 (tt) REVERT: C 259 ILE cc_start: 0.8009 (mm) cc_final: 0.7369 (pt) REVERT: C 321 ASP cc_start: 0.6915 (t0) cc_final: 0.6662 (t0) outliers start: 35 outliers final: 28 residues processed: 252 average time/residue: 0.2959 time to fit residues: 114.0782 Evaluate side-chains 248 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 148 optimal weight: 0.1980 chunk 143 optimal weight: 0.1980 chunk 131 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 218 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.087963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071666 restraints weight = 49532.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071849 restraints weight = 42320.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.072506 restraints weight = 34627.205| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 18004 Z= 0.107 Angle : 0.512 10.768 24467 Z= 0.266 Chirality : 0.041 0.228 2786 Planarity : 0.003 0.045 3061 Dihedral : 6.638 73.189 2761 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.01 % Allowed : 14.42 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2209 helix: 1.76 (0.18), residues: 873 sheet: -0.61 (0.28), residues: 356 loop : -1.30 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 530 HIS 0.004 0.001 HIS B 359 PHE 0.034 0.001 PHE B 789 TYR 0.014 0.001 TYR B 751 ARG 0.004 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 7) link_NAG-ASN : angle 1.37571 ( 21) link_BETA1-4 : bond 0.00338 ( 3) link_BETA1-4 : angle 1.08085 ( 9) hydrogen bonds : bond 0.04132 ( 732) hydrogen bonds : angle 3.86109 ( 2106) SS BOND : bond 0.00237 ( 18) SS BOND : angle 1.78088 ( 36) covalent geometry : bond 0.00241 (17976) covalent geometry : angle 0.50629 (24401) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7746 (m100) cc_final: 0.7379 (m100) REVERT: D 334 SER cc_start: 0.6453 (p) cc_final: 0.6041 (p) REVERT: E 21 MET cc_start: 0.7223 (ppp) cc_final: 0.6301 (ttp) REVERT: A 719 TRP cc_start: 0.6819 (t60) cc_final: 0.6204 (t-100) REVERT: A 745 THR cc_start: 0.8380 (t) cc_final: 0.8056 (t) REVERT: A 760 ILE cc_start: 0.8672 (mt) cc_final: 0.8384 (mm) REVERT: A 790 PHE cc_start: 0.8129 (m-10) cc_final: 0.7772 (m-80) REVERT: A 832 PHE cc_start: 0.6911 (m-10) cc_final: 0.6679 (m-80) REVERT: B 446 ASN cc_start: 0.7794 (t0) cc_final: 0.7369 (t0) REVERT: B 558 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7679 (mm-30) REVERT: C 29 LEU cc_start: 0.8831 (tp) cc_final: 0.8601 (tt) REVERT: C 212 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7250 (mm-30) REVERT: C 259 ILE cc_start: 0.7945 (mm) cc_final: 0.7337 (pt) REVERT: C 321 ASP cc_start: 0.6919 (t0) cc_final: 0.6622 (t0) outliers start: 36 outliers final: 26 residues processed: 244 average time/residue: 0.2846 time to fit residues: 106.3703 Evaluate side-chains 251 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 196 optimal weight: 6.9990 chunk 166 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 120 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.088081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071691 restraints weight = 50030.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071773 restraints weight = 42587.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072530 restraints weight = 34984.889| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 18004 Z= 0.108 Angle : 0.522 12.358 24467 Z= 0.269 Chirality : 0.041 0.229 2786 Planarity : 0.003 0.046 3061 Dihedral : 6.519 71.921 2761 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.79 % Allowed : 15.26 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2209 helix: 1.80 (0.18), residues: 873 sheet: -0.61 (0.28), residues: 366 loop : -1.27 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 169 HIS 0.005 0.001 HIS C 218 PHE 0.036 0.001 PHE B 789 TYR 0.015 0.001 TYR B 751 ARG 0.004 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 7) link_NAG-ASN : angle 1.36139 ( 21) link_BETA1-4 : bond 0.00427 ( 3) link_BETA1-4 : angle 1.11271 ( 9) hydrogen bonds : bond 0.04081 ( 732) hydrogen bonds : angle 3.82944 ( 2106) SS BOND : bond 0.00246 ( 18) SS BOND : angle 1.83299 ( 36) covalent geometry : bond 0.00245 (17976) covalent geometry : angle 0.51613 (24401) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7759 (m100) cc_final: 0.7371 (m100) REVERT: D 334 SER cc_start: 0.6450 (p) cc_final: 0.6031 (p) REVERT: A 719 TRP cc_start: 0.6820 (t60) cc_final: 0.6206 (t-100) REVERT: A 745 THR cc_start: 0.8359 (t) cc_final: 0.8027 (t) REVERT: A 760 ILE cc_start: 0.8667 (mt) cc_final: 0.8368 (mm) REVERT: A 790 PHE cc_start: 0.8144 (m-10) cc_final: 0.7766 (m-80) REVERT: A 832 PHE cc_start: 0.6903 (m-10) cc_final: 0.6663 (m-80) REVERT: B 446 ASN cc_start: 0.7825 (t0) cc_final: 0.7309 (t0) REVERT: B 558 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7703 (mm-30) REVERT: B 733 PHE cc_start: 0.7169 (t80) cc_final: 0.6940 (t80) REVERT: C 29 LEU cc_start: 0.8851 (tp) cc_final: 0.8621 (tt) REVERT: C 203 MET cc_start: 0.7102 (tpp) cc_final: 0.6683 (mmt) REVERT: C 259 ILE cc_start: 0.7939 (mm) cc_final: 0.7331 (pt) REVERT: C 321 ASP cc_start: 0.6888 (t0) cc_final: 0.6572 (t0) outliers start: 32 outliers final: 23 residues processed: 247 average time/residue: 0.3092 time to fit residues: 117.5688 Evaluate side-chains 248 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 174 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.087690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.071180 restraints weight = 49643.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071308 restraints weight = 42208.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.071913 restraints weight = 35912.501| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18004 Z= 0.143 Angle : 0.547 10.617 24467 Z= 0.284 Chirality : 0.043 0.231 2786 Planarity : 0.004 0.045 3061 Dihedral : 6.500 72.339 2761 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.51 % Allowed : 15.93 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2209 helix: 1.65 (0.18), residues: 878 sheet: -0.61 (0.28), residues: 365 loop : -1.30 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 818 HIS 0.004 0.001 HIS A 429 PHE 0.015 0.001 PHE B 619 TYR 0.023 0.001 TYR E 40 ARG 0.004 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 7) link_NAG-ASN : angle 1.50184 ( 21) link_BETA1-4 : bond 0.00309 ( 3) link_BETA1-4 : angle 1.18109 ( 9) hydrogen bonds : bond 0.04614 ( 732) hydrogen bonds : angle 3.90444 ( 2106) SS BOND : bond 0.00164 ( 18) SS BOND : angle 1.01568 ( 36) covalent geometry : bond 0.00338 (17976) covalent geometry : angle 0.54399 (24401) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7816 (m100) cc_final: 0.7441 (m100) REVERT: D 139 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6949 (mt) REVERT: D 334 SER cc_start: 0.6494 (p) cc_final: 0.6061 (p) REVERT: E 21 MET cc_start: 0.7226 (ppp) cc_final: 0.6383 (ttp) REVERT: A 719 TRP cc_start: 0.6857 (t60) cc_final: 0.6262 (t-100) REVERT: A 745 THR cc_start: 0.8312 (t) cc_final: 0.7989 (t) REVERT: A 760 ILE cc_start: 0.8656 (mt) cc_final: 0.8362 (mm) REVERT: A 790 PHE cc_start: 0.8164 (m-10) cc_final: 0.7823 (m-80) REVERT: A 832 PHE cc_start: 0.6959 (m-10) cc_final: 0.6703 (m-80) REVERT: B 446 ASN cc_start: 0.7809 (t0) cc_final: 0.7279 (t0) REVERT: B 558 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 733 PHE cc_start: 0.7233 (t80) cc_final: 0.6953 (t80) REVERT: C 29 LEU cc_start: 0.8857 (tp) cc_final: 0.8626 (tt) REVERT: C 203 MET cc_start: 0.7095 (tpp) cc_final: 0.6680 (mmt) REVERT: C 259 ILE cc_start: 0.7946 (mm) cc_final: 0.7351 (pt) REVERT: C 306 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5587 (ptp-170) REVERT: C 321 ASP cc_start: 0.6896 (t0) cc_final: 0.6684 (t0) outliers start: 27 outliers final: 23 residues processed: 243 average time/residue: 0.2894 time to fit residues: 107.3533 Evaluate side-chains 253 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 23 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 128 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.087815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071453 restraints weight = 49805.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.071588 restraints weight = 42490.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072318 restraints weight = 35873.939| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18004 Z= 0.115 Angle : 0.530 10.823 24467 Z= 0.273 Chirality : 0.042 0.229 2786 Planarity : 0.003 0.045 3061 Dihedral : 6.262 71.311 2761 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.73 % Allowed : 15.76 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.18), residues: 2209 helix: 1.73 (0.18), residues: 877 sheet: -0.60 (0.28), residues: 356 loop : -1.28 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 169 HIS 0.004 0.001 HIS B 359 PHE 0.015 0.001 PHE B 619 TYR 0.022 0.001 TYR E 40 ARG 0.009 0.000 ARG C 256 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 7) link_NAG-ASN : angle 1.40171 ( 21) link_BETA1-4 : bond 0.00313 ( 3) link_BETA1-4 : angle 1.07665 ( 9) hydrogen bonds : bond 0.04208 ( 732) hydrogen bonds : angle 3.83521 ( 2106) SS BOND : bond 0.00147 ( 18) SS BOND : angle 0.86487 ( 36) covalent geometry : bond 0.00262 (17976) covalent geometry : angle 0.52752 (24401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5215.61 seconds wall clock time: 92 minutes 47.60 seconds (5567.60 seconds total)