Starting phenix.real_space_refine on Sun Jun 15 17:41:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szg_40915/06_2025/8szg_40915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szg_40915/06_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_40915/06_2025/8szg_40915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szg_40915/06_2025/8szg_40915.map" model { file = "/net/cci-nas-00/data/ceres_data/8szg_40915/06_2025/8szg_40915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szg_40915/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.55, per 1000 atoms: 0.77 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: 4.44 Conformation dependent library (CDL) restraints added in 2.2 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: 1.93 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: 6.17 Time building geometry restraints manager: 5.22 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: 0.010 Normalize map: mean=0, sd=1: 73.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 44.370 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.560 ------------------------------------------------------------------------------- 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 : 1.886 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: 0.3070 time to fit residues: 139.3163 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 : 2.134 ------------------------------------------------------------------------------- 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 = 0.072790 restraints weight = 40126.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073292 restraints weight = 38919.445| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 2.156 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: 0.7324 (m100) REVERT: A 760 ILE cc_start: 0.8658 (mt) cc_final: 0.8327 (mm) REVERT: A 789 PHE cc_start: 0.8530 (t80) cc_final: 0.8214 (t80) REVERT: A 790 PHE cc_start: 0.8012 (m-10) cc_final: 0.7657 (m-80) REVERT: A 829 TYR cc_start: 0.7987 (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: 0.8247 (mm) REVERT: C 29 LEU cc_start: 0.8805 (tp) cc_final: 0.8539 (tt) REVERT: C 252 LYS cc_start: 0.7304 (mtpp) cc_final: 0.7002 (mtpp) REVERT: C 259 ILE cc_start: 0.8123 (mm) cc_final: 0.7469 (pt) REVERT: C 316 LEU cc_start: 0.8000 (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: 0.3250 time to fit residues: 126.2506 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 : 2.056 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.9980 chunk 111 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 700 ASN B 800 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.087374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.071203 restraints weight = 49488.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071441 restraints weight = 39863.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.071898 restraints weight = 38194.269| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18004 Z= 0.154 Angle : 0.551 12.034 24467 Z= 0.290 Chirality : 0.043 0.233 2786 Planarity : 0.004 0.044 3061 Dihedral : 8.251 80.966 2761 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.51 % Allowed : 10.73 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2209 helix: 1.43 (0.18), residues: 882 sheet: -0.73 (0.28), residues: 365 loop : -1.31 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 818 HIS 0.006 0.001 HIS B 359 PHE 0.017 0.001 PHE A 814 TYR 0.014 0.001 TYR E 40 ARG 0.006 0.000 ARG A 873 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 7) link_NAG-ASN : angle 1.53959 ( 21) link_BETA1-4 : bond 0.00436 ( 3) link_BETA1-4 : angle 1.27191 ( 9) hydrogen bonds : bond 0.05420 ( 732) hydrogen bonds : angle 4.27228 ( 2106) SS BOND : bond 0.00185 ( 18) SS BOND : angle 1.84952 ( 36) covalent geometry : bond 0.00359 (17976) covalent geometry : angle 0.54448 (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 268 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7731 (m100) cc_final: 0.7352 (m100) REVERT: D 234 PHE cc_start: 0.5260 (t80) cc_final: 0.4890 (t80) REVERT: A 760 ILE cc_start: 0.8639 (mt) cc_final: 0.8333 (mm) REVERT: A 790 PHE cc_start: 0.8091 (m-10) cc_final: 0.7717 (m-80) REVERT: A 829 TYR cc_start: 0.7998 (p90) cc_final: 0.7731 (p90) REVERT: A 832 PHE cc_start: 0.7076 (m-10) cc_final: 0.6825 (m-80) REVERT: B 446 ASN cc_start: 0.7774 (t0) cc_final: 0.7428 (t0) REVERT: B 558 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 738 ILE cc_start: 0.7434 (tp) cc_final: 0.7162 (tt) REVERT: C 27 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7293 (ptp-170) REVERT: C 29 LEU cc_start: 0.8804 (tp) cc_final: 0.8547 (tt) REVERT: C 252 LYS cc_start: 0.7286 (mtpp) cc_final: 0.6893 (mtmm) REVERT: C 259 ILE cc_start: 0.8146 (mm) cc_final: 0.7479 (pt) REVERT: C 312 MET cc_start: 0.8194 (tpp) cc_final: 0.7912 (tmm) REVERT: C 321 ASP cc_start: 0.7082 (t0) cc_final: 0.6870 (t0) outliers start: 27 outliers final: 17 residues processed: 253 average time/residue: 0.3146 time to fit residues: 119.2895 Evaluate side-chains 247 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 2.159 ------------------------------------------------------------------------------- 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 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 740 VAL 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: 4.9990 chunk 1 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 72 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.088075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071884 restraints weight = 49749.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.072184 restraints weight = 40527.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.072774 restraints weight = 34339.861| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1658 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= 0.117 Angle : 0.505 10.209 24467 Z= 0.265 Chirality : 0.042 0.229 2786 Planarity : 0.004 0.044 3061 Dihedral : 7.687 77.532 2761 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.45 % Allowed : 12.07 % Favored : 86.47 % 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: -0.06 (0.18), residues: 2209 helix: 1.56 (0.18), residues: 881 sheet: -0.64 (0.28), residues: 355 loop : -1.32 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 263 HIS 0.005 0.001 HIS B 359 PHE 0.019 0.001 PHE A 625 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 0.00158 ( 7) link_NAG-ASN : angle 1.42501 ( 21) link_BETA1-4 : bond 0.00369 ( 3) link_BETA1-4 : angle 1.11352 ( 9) hydrogen bonds : bond 0.04604 ( 732) hydrogen bonds : angle 4.05596 ( 2106) SS BOND : bond 0.00158 ( 18) SS BOND : angle 1.12510 ( 36) covalent geometry : bond 0.00261 (17976) covalent geometry : angle 0.50135 (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: 26 poor density : 238 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7754 (m100) cc_final: 0.7397 (m100) REVERT: D 234 PHE cc_start: 0.5186 (t80) cc_final: 0.4872 (t80) REVERT: A 760 ILE cc_start: 0.8644 (mt) cc_final: 0.8291 (mm) REVERT: A 790 PHE cc_start: 0.8061 (m-10) cc_final: 0.7723 (m-10) REVERT: A 829 TYR cc_start: 0.7960 (p90) cc_final: 0.7728 (p90) REVERT: A 832 PHE cc_start: 0.6999 (m-10) cc_final: 0.6752 (m-80) REVERT: B 446 ASN cc_start: 0.7764 (t0) cc_final: 0.7383 (t0) REVERT: B 558 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 738 ILE cc_start: 0.7527 (tp) cc_final: 0.7296 (tp) REVERT: C 29 LEU cc_start: 0.8801 (tp) cc_final: 0.8531 (tt) REVERT: C 212 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6866 (mm-30) REVERT: C 259 ILE cc_start: 0.8090 (mm) cc_final: 0.7413 (pt) outliers start: 26 outliers final: 20 residues processed: 249 average time/residue: 0.3080 time to fit residues: 116.0327 Evaluate side-chains 249 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 1.955 ------------------------------------------------------------------------------- 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 547 LEU 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 733 PHE 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 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: 9.9990 chunk 175 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 chunk 145 optimal weight: 0.0980 chunk 134 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 = 0.087732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071461 restraints weight = 50167.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071360 restraints weight = 45369.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.072074 restraints weight = 38951.434| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18004 Z= 0.114 Angle : 0.502 13.127 24467 Z= 0.261 Chirality : 0.041 0.230 2786 Planarity : 0.003 0.045 3061 Dihedral : 7.233 77.097 2761 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.68 % Allowed : 12.97 % Favored : 85.35 % 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: -0.03 (0.18), residues: 2209 helix: 1.61 (0.18), residues: 878 sheet: -0.76 (0.28), residues: 365 loop : -1.27 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 263 HIS 0.004 0.001 HIS B 359 PHE 0.014 0.001 PHE B 814 TYR 0.013 0.001 TYR B 751 ARG 0.006 0.000 ARG E 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 7) link_NAG-ASN : angle 1.39194 ( 21) link_BETA1-4 : bond 0.00334 ( 3) link_BETA1-4 : angle 1.10987 ( 9) hydrogen bonds : bond 0.04431 ( 732) hydrogen bonds : angle 3.97919 ( 2106) SS BOND : bond 0.00242 ( 18) SS BOND : angle 1.41867 ( 36) covalent geometry : bond 0.00257 (17976) covalent geometry : angle 0.49788 (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 272 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7702 (m100) cc_final: 0.7350 (m100) REVERT: D 234 PHE cc_start: 0.5352 (t80) cc_final: 0.5079 (t80) REVERT: D 334 SER cc_start: 0.6557 (p) cc_final: 0.6144 (p) REVERT: A 760 ILE cc_start: 0.8648 (mt) cc_final: 0.8356 (mm) REVERT: A 790 PHE cc_start: 0.8055 (m-10) cc_final: 0.7683 (m-80) REVERT: A 829 TYR cc_start: 0.7953 (p90) cc_final: 0.7746 (p90) REVERT: A 832 PHE cc_start: 0.6970 (m-10) cc_final: 0.6742 (m-80) REVERT: B 446 ASN cc_start: 0.7769 (t0) cc_final: 0.7333 (t0) REVERT: B 558 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 738 ILE cc_start: 0.7522 (tp) cc_final: 0.7314 (tp) REVERT: C 29 LEU cc_start: 0.8803 (tp) cc_final: 0.8530 (tt) REVERT: C 252 LYS cc_start: 0.7452 (mtpp) cc_final: 0.6963 (mtmm) REVERT: C 259 ILE cc_start: 0.8078 (mm) cc_final: 0.7416 (pt) REVERT: C 311 LYS cc_start: 0.7928 (tmtt) cc_final: 0.7589 (tmtt) REVERT: C 312 MET cc_start: 0.8152 (tpp) cc_final: 0.7940 (tmm) REVERT: C 321 ASP cc_start: 0.6811 (t0) cc_final: 0.6549 (t0) REVERT: C 322 LYS cc_start: 0.6562 (ptmm) cc_final: 0.6215 (pttp) outliers start: 30 outliers final: 23 residues processed: 252 average time/residue: 0.3006 time to fit residues: 115.4701 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 : 2.192 ------------------------------------------------------------------------------- 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 547 LEU 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 270 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 733 PHE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 58 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.088149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071919 restraints weight = 49621.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071866 restraints weight = 43303.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.072483 restraints weight = 39447.474| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18004 Z= 0.106 Angle : 0.499 11.718 24467 Z= 0.259 Chirality : 0.041 0.228 2786 Planarity : 0.003 0.045 3061 Dihedral : 6.858 75.371 2761 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.96 % Allowed : 13.97 % Favored : 84.07 % 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: 1.74 (0.18), residues: 873 sheet: -0.59 (0.28), residues: 361 loop : -1.29 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 263 HIS 0.004 0.001 HIS B 359 PHE 0.030 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 0.00150 ( 7) link_NAG-ASN : angle 1.36167 ( 21) link_BETA1-4 : bond 0.00315 ( 3) link_BETA1-4 : angle 1.05943 ( 9) hydrogen bonds : bond 0.04143 ( 732) hydrogen bonds : angle 3.89080 ( 2106) SS BOND : bond 0.00150 ( 18) SS BOND : angle 1.23565 ( 36) covalent geometry : bond 0.00236 (17976) covalent geometry : angle 0.49559 (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 268 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7725 (m100) cc_final: 0.7354 (m100) REVERT: D 334 SER cc_start: 0.6485 (p) cc_final: 0.6069 (p) REVERT: E 21 MET cc_start: 0.7178 (ppp) cc_final: 0.6207 (ttp) REVERT: A 719 TRP cc_start: 0.6815 (t60) cc_final: 0.6215 (t-100) REVERT: A 760 ILE cc_start: 0.8673 (mt) cc_final: 0.8383 (mm) REVERT: A 790 PHE cc_start: 0.8077 (m-10) cc_final: 0.7718 (m-80) REVERT: A 829 TYR cc_start: 0.7942 (p90) cc_final: 0.7714 (p90) REVERT: A 832 PHE cc_start: 0.6946 (m-10) cc_final: 0.6720 (m-80) REVERT: B 446 ASN cc_start: 0.7784 (t0) cc_final: 0.7495 (t0) REVERT: B 558 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7680 (mm-30) REVERT: C 29 LEU cc_start: 0.8812 (tp) cc_final: 0.8593 (tt) REVERT: C 212 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7155 (mm-30) REVERT: C 252 LYS cc_start: 0.7429 (mtpp) cc_final: 0.6969 (mtmm) REVERT: C 259 ILE cc_start: 0.8017 (mm) cc_final: 0.7382 (pt) REVERT: C 311 LYS cc_start: 0.7905 (tmtt) cc_final: 0.7619 (tmtt) REVERT: C 312 MET cc_start: 0.8135 (tpp) cc_final: 0.7926 (tmm) REVERT: C 321 ASP cc_start: 0.6883 (t0) cc_final: 0.6598 (t0) REVERT: C 322 LYS cc_start: 0.6503 (ptmm) cc_final: 0.6226 (pttp) outliers start: 35 outliers final: 25 residues processed: 247 average time/residue: 0.2971 time to fit residues: 111.4704 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 : 1.922 ------------------------------------------------------------------------------- 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 429 HIS Chi-restraints excluded: chain A residue 547 LEU 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 A residue 869 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 666 LEU Chi-restraints excluded: chain B residue 697 VAL 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 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 218 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.088107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.071785 restraints weight = 49634.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071944 restraints weight = 44317.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072469 restraints weight = 40101.699| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18004 Z= 0.124 Angle : 0.509 11.306 24467 Z= 0.266 Chirality : 0.042 0.230 2786 Planarity : 0.003 0.045 3061 Dihedral : 6.734 74.016 2761 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.12 % Allowed : 13.86 % Favored : 84.01 % 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: 1.65 (0.18), residues: 881 sheet: -0.63 (0.28), residues: 356 loop : -1.29 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 169 HIS 0.011 0.001 HIS C 218 PHE 0.028 0.001 PHE B 789 TYR 0.012 0.001 TYR B 421 ARG 0.003 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 7) link_NAG-ASN : angle 1.40751 ( 21) link_BETA1-4 : bond 0.00307 ( 3) link_BETA1-4 : angle 1.11335 ( 9) hydrogen bonds : bond 0.04368 ( 732) hydrogen bonds : angle 3.91775 ( 2106) SS BOND : bond 0.00314 ( 18) SS BOND : angle 1.54055 ( 36) covalent geometry : bond 0.00288 (17976) covalent geometry : angle 0.50399 (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 267 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7760 (m100) cc_final: 0.7390 (m100) REVERT: D 334 SER cc_start: 0.6504 (p) cc_final: 0.6088 (p) REVERT: A 719 TRP cc_start: 0.6836 (t60) cc_final: 0.6237 (t-100) REVERT: A 760 ILE cc_start: 0.8677 (mt) cc_final: 0.8386 (mm) REVERT: A 790 PHE cc_start: 0.8125 (m-10) cc_final: 0.7773 (m-80) REVERT: A 832 PHE cc_start: 0.6980 (m-10) cc_final: 0.6716 (m-80) REVERT: B 446 ASN cc_start: 0.7780 (t0) cc_final: 0.7307 (t0) REVERT: B 558 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7687 (mm-30) REVERT: C 29 LEU cc_start: 0.8826 (tp) cc_final: 0.8609 (tt) REVERT: C 203 MET cc_start: 0.7474 (mmm) cc_final: 0.7263 (mmt) REVERT: C 259 ILE cc_start: 0.8017 (mm) cc_final: 0.7358 (pt) REVERT: C 312 MET cc_start: 0.8145 (tpp) cc_final: 0.7859 (tmm) REVERT: C 321 ASP cc_start: 0.6871 (t0) cc_final: 0.6589 (t0) REVERT: C 322 LYS cc_start: 0.6514 (ptmm) cc_final: 0.6273 (pttp) outliers start: 38 outliers final: 31 residues processed: 246 average time/residue: 0.3037 time to fit residues: 113.8310 Evaluate side-chains 256 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 2.074 ------------------------------------------------------------------------------- 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 744 TYR 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 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 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 733 PHE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 148 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 84 optimal weight: 0.0030 chunk 184 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.088242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071864 restraints weight = 49462.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.072090 restraints weight = 42747.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072726 restraints weight = 36079.322| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18004 Z= 0.117 Angle : 0.513 10.624 24467 Z= 0.268 Chirality : 0.042 0.229 2786 Planarity : 0.003 0.045 3061 Dihedral : 6.559 72.952 2761 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.40 % Allowed : 14.37 % Favored : 83.23 % 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: 1.67 (0.18), residues: 880 sheet: -0.62 (0.28), residues: 356 loop : -1.28 (0.19), residues: 973 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 0.031 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 0.00136 ( 7) link_NAG-ASN : angle 1.40857 ( 21) link_BETA1-4 : bond 0.00293 ( 3) link_BETA1-4 : angle 1.09652 ( 9) hydrogen bonds : bond 0.04292 ( 732) hydrogen bonds : angle 3.90847 ( 2106) SS BOND : bond 0.00231 ( 18) SS BOND : angle 1.33569 ( 36) covalent geometry : bond 0.00266 (17976) covalent geometry : angle 0.50941 (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 271 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7729 (m100) cc_final: 0.7358 (m100) REVERT: D 334 SER cc_start: 0.6465 (p) cc_final: 0.6045 (p) REVERT: E 21 MET cc_start: 0.7167 (ppp) cc_final: 0.6300 (ttp) REVERT: A 719 TRP cc_start: 0.6786 (t60) cc_final: 0.6194 (t-100) REVERT: A 760 ILE cc_start: 0.8683 (mt) cc_final: 0.8404 (mm) REVERT: A 790 PHE cc_start: 0.8128 (m-10) cc_final: 0.7745 (m-80) REVERT: A 832 PHE cc_start: 0.6923 (m-10) cc_final: 0.6685 (m-80) REVERT: B 446 ASN cc_start: 0.7776 (t0) cc_final: 0.7339 (t0) REVERT: B 558 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7685 (mm-30) REVERT: C 29 LEU cc_start: 0.8824 (tp) cc_final: 0.8602 (tt) REVERT: C 259 ILE cc_start: 0.8009 (mm) cc_final: 0.7377 (pt) REVERT: C 321 ASP cc_start: 0.6898 (t0) cc_final: 0.6628 (t0) REVERT: C 322 LYS cc_start: 0.6517 (ptmm) cc_final: 0.6235 (pttp) outliers start: 43 outliers final: 31 residues processed: 249 average time/residue: 0.3030 time to fit residues: 115.2559 Evaluate side-chains 257 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 744 TYR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 782 LEU 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 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL 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 733 PHE 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 344 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 196 optimal weight: 7.9990 chunk 166 optimal weight: 0.0040 chunk 138 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 125 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 191 optimal weight: 0.0870 chunk 115 optimal weight: 0.9990 overall best weight: 0.4570 ------------------------------------------------------------------------------- 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 C 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.089004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072509 restraints weight = 50111.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072809 restraints weight = 41537.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073370 restraints weight = 35465.503| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 18004 Z= 0.101 Angle : 0.505 10.871 24467 Z= 0.261 Chirality : 0.041 0.229 2786 Planarity : 0.003 0.045 3061 Dihedral : 6.283 70.479 2761 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.90 % Allowed : 14.87 % Favored : 83.23 % 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: 0.14 (0.18), residues: 2209 helix: 1.77 (0.18), residues: 877 sheet: -0.57 (0.28), residues: 355 loop : -1.22 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 299 HIS 0.004 0.001 HIS B 359 PHE 0.039 0.001 PHE B 789 TYR 0.011 0.001 TYR B 751 ARG 0.004 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 7) link_NAG-ASN : angle 1.32143 ( 21) link_BETA1-4 : bond 0.00381 ( 3) link_BETA1-4 : angle 1.06583 ( 9) hydrogen bonds : bond 0.03885 ( 732) hydrogen bonds : angle 3.79786 ( 2106) SS BOND : bond 0.00293 ( 18) SS BOND : angle 1.59689 ( 36) covalent geometry : bond 0.00224 (17976) covalent geometry : angle 0.50052 (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 266 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7714 (m100) cc_final: 0.7314 (m100) REVERT: D 334 SER cc_start: 0.6380 (p) cc_final: 0.5963 (p) REVERT: E 13 ARG cc_start: 0.6391 (tpm170) cc_final: 0.6139 (tpt90) REVERT: E 21 MET cc_start: 0.7193 (ppp) cc_final: 0.6374 (ttp) REVERT: A 719 TRP cc_start: 0.6828 (t60) cc_final: 0.6191 (t-100) REVERT: A 745 THR cc_start: 0.8352 (t) cc_final: 0.8027 (t) REVERT: A 760 ILE cc_start: 0.8690 (mt) cc_final: 0.8402 (mm) REVERT: A 790 PHE cc_start: 0.8078 (m-10) cc_final: 0.7678 (m-80) REVERT: A 832 PHE cc_start: 0.6863 (m-10) cc_final: 0.6608 (m-80) REVERT: B 446 ASN cc_start: 0.7804 (t0) cc_final: 0.7283 (t0) REVERT: B 558 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7693 (mm-30) REVERT: B 733 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6900 (t80) REVERT: C 29 LEU cc_start: 0.8833 (tp) cc_final: 0.8601 (tt) REVERT: C 259 ILE cc_start: 0.7948 (mm) cc_final: 0.7341 (pt) REVERT: C 321 ASP cc_start: 0.6845 (t0) cc_final: 0.6630 (t0) outliers start: 34 outliers final: 26 residues processed: 250 average time/residue: 0.2897 time to fit residues: 111.1983 Evaluate side-chains 254 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 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 A residue 865 SER 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 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 733 PHE 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 783 LEU Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 218 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 108 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 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: 0.6980 chunk 100 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.087890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.071822 restraints weight = 49642.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071743 restraints weight = 45048.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.072339 restraints weight = 41934.388| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18004 Z= 0.146 Angle : 0.555 11.146 24467 Z= 0.288 Chirality : 0.043 0.248 2786 Planarity : 0.004 0.044 3061 Dihedral : 6.283 70.887 2761 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: 0.06 (0.18), residues: 2209 helix: 1.69 (0.18), residues: 878 sheet: -0.59 (0.28), residues: 354 loop : -1.27 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 818 HIS 0.009 0.001 HIS C 218 PHE 0.035 0.001 PHE B 789 TYR 0.024 0.001 TYR E 40 ARG 0.005 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 7) link_NAG-ASN : angle 1.46245 ( 21) link_BETA1-4 : bond 0.00279 ( 3) link_BETA1-4 : angle 1.18130 ( 9) hydrogen bonds : bond 0.04574 ( 732) hydrogen bonds : angle 3.88774 ( 2106) SS BOND : bond 0.00191 ( 18) SS BOND : angle 1.92051 ( 36) covalent geometry : bond 0.00348 (17976) covalent geometry : angle 0.54835 (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 261 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7721 (m100) cc_final: 0.7357 (m100) REVERT: D 139 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6925 (mt) REVERT: D 334 SER cc_start: 0.6432 (p) cc_final: 0.6014 (p) REVERT: E 13 ARG cc_start: 0.6313 (tpm170) cc_final: 0.6067 (tpt90) REVERT: E 21 MET cc_start: 0.7177 (ppp) cc_final: 0.6385 (ttp) REVERT: A 719 TRP cc_start: 0.6811 (t60) cc_final: 0.6248 (t-100) REVERT: A 745 THR cc_start: 0.8269 (t) cc_final: 0.7941 (t) REVERT: A 760 ILE cc_start: 0.8677 (mt) cc_final: 0.8405 (mm) REVERT: A 790 PHE cc_start: 0.8153 (m-10) cc_final: 0.7790 (m-80) REVERT: A 832 PHE cc_start: 0.6925 (m-10) cc_final: 0.6641 (m-80) REVERT: B 446 ASN cc_start: 0.7756 (t0) cc_final: 0.7236 (t0) REVERT: B 558 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7702 (mm-30) REVERT: B 733 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.7014 (t80) REVERT: C 29 LEU cc_start: 0.8801 (tp) cc_final: 0.8582 (tt) REVERT: C 259 ILE cc_start: 0.7989 (mm) cc_final: 0.7369 (pt) REVERT: C 321 ASP cc_start: 0.6929 (t0) cc_final: 0.6625 (t0) outliers start: 32 outliers final: 26 residues processed: 243 average time/residue: 0.2978 time to fit residues: 110.9583 Evaluate side-chains 259 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 1.915 ------------------------------------------------------------------------------- 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 250 GLU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 703 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 A residue 782 LEU 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 627 THR Chi-restraints excluded: chain B residue 635 ILE 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 733 PHE 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 783 LEU Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 23 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.088037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071685 restraints weight = 49806.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.071824 restraints weight = 43029.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072441 restraints weight = 37510.940| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18004 Z= 0.131 Angle : 0.549 14.256 24467 Z= 0.283 Chirality : 0.042 0.231 2786 Planarity : 0.003 0.045 3061 Dihedral : 6.220 70.760 2761 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.68 % Allowed : 15.37 % 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: 0.05 (0.18), residues: 2209 helix: 1.69 (0.18), residues: 878 sheet: -0.59 (0.28), residues: 354 loop : -1.29 (0.19), residues: 977 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 0.036 0.001 PHE B 789 TYR 0.021 0.001 TYR E 40 ARG 0.004 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 7) link_NAG-ASN : angle 1.44440 ( 21) link_BETA1-4 : bond 0.00309 ( 3) link_BETA1-4 : angle 1.11723 ( 9) hydrogen bonds : bond 0.04474 ( 732) hydrogen bonds : angle 3.88221 ( 2106) SS BOND : bond 0.00292 ( 18) SS BOND : angle 1.76106 ( 36) covalent geometry : bond 0.00308 (17976) covalent geometry : angle 0.54374 (24401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6124.40 seconds wall clock time: 108 minutes 15.14 seconds (6495.14 seconds total)