Starting phenix.real_space_refine on Mon May 26 19:01:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vuu_43540/05_2025/8vuu_43540.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vuu_43540/05_2025/8vuu_43540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vuu_43540/05_2025/8vuu_43540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vuu_43540/05_2025/8vuu_43540.map" model { file = "/net/cci-nas-00/data/ceres_data/8vuu_43540/05_2025/8vuu_43540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vuu_43540/05_2025/8vuu_43540.cif" } resolution = 4.05 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= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 291 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 18253 2.51 5 N 4912 2.21 5 O 5323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 1.64s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28618 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6048 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 35, 'TRANS': 766} Chain breaks: 1 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 193 Chain: "B" Number of atoms: 5636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5636 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 29, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 600 Unresolved non-hydrogen angles: 756 Unresolved non-hydrogen dihedrals: 496 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 21, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 26, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 378 Chain: "C" Number of atoms: 5777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 5777 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 35, 'TRANS': 766} Chain breaks: 1 Unresolved non-hydrogen bonds: 561 Unresolved non-hydrogen angles: 696 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 19, 'PHE:plan': 5, 'GLU:plan': 29, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 354 Chain: "D" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5146 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 289} Link IDs: {'PTRANS': 28, 'TRANS': 755} Chain breaks: 3 Unresolved non-hydrogen bonds: 1082 Unresolved non-hydrogen angles: 1378 Unresolved non-hydrogen dihedrals: 886 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 35, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 12, 'GLU:plan': 39, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 655 Chain: "H" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1507 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 197} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "J" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1450 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 196} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "K" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1511 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "L" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1543 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 17.74, per 1000 atoms: 0.62 Number of scatterers: 28618 At special positions: 0 Unit cell: (118.128, 148.944, 250.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 5323 8.00 N 4912 7.00 C 18253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=1.93 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 137 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 137 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 136 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " 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 Time building additional restraints: 7.32 Conformation dependent library (CDL) restraints added in 4.7 seconds 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7504 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 49 sheets defined 33.5% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 35 through 54 removed outlier: 3.699A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 removed outlier: 4.047A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.716A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.832A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 removed outlier: 4.043A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 4.192A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.645A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.626A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.613A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.838A pdb=" N PHE A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 522 through 526 removed outlier: 4.022A pdb=" N GLN A 525 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 526 " --> pdb=" O ARG A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 522 through 526' Processing helix chain 'A' and resid 561 through 579 Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.810A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 657 removed outlier: 3.759A pdb=" N THR A 648 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 649 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 668 removed outlier: 3.581A pdb=" N ASN A 668 " --> pdb=" O THR A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.893A pdb=" N ARG A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.737A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.970A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 723 removed outlier: 3.800A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 769 through 782 removed outlier: 3.784A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 812 through 841 removed outlier: 3.715A pdb=" N GLY A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 823 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 removed outlier: 3.558A pdb=" N ASP B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 106 through 120 removed outlier: 4.326A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 4.054A pdb=" N SER B 131 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.611A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 233 through 247 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 288 through 310 removed outlier: 4.046A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.615A pdb=" N ASN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 473 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.560A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 579 removed outlier: 3.734A pdb=" N MET B 561 " --> pdb=" O ASP B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 614 Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.738A pdb=" N ILE B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 698 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 772 through 787 removed outlier: 3.584A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 4.278A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 843 Processing helix chain 'C' and resid 36 through 53 removed outlier: 3.984A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'C' and resid 105 through 110 removed outlier: 4.149A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.656A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 removed outlier: 4.647A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.574A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.735A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 Processing helix chain 'C' and resid 317 through 326 removed outlier: 3.783A pdb=" N LYS C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.927A pdb=" N GLY C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.565A pdb=" N ALA C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 584 removed outlier: 3.701A pdb=" N GLY C 567 " --> pdb=" O TRP C 563 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 615 removed outlier: 4.409A pdb=" N SER C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP C 611 " --> pdb=" O MET C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.696A pdb=" N ILE C 631 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER C 646 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.945A pdb=" N TYR C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 709 Processing helix chain 'C' and resid 715 through 723 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 809 through 812 Processing helix chain 'C' and resid 813 through 841 removed outlier: 3.574A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.894A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 106 through 119 removed outlier: 4.255A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.796A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 193 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.935A pdb=" N THR D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.739A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 259 through 264' Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 323 through 329 removed outlier: 3.751A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 340 removed outlier: 3.754A pdb=" N ARG D 337 " --> pdb=" O ASN D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 473 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.807A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 614 removed outlier: 3.573A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 654 removed outlier: 4.319A pdb=" N ILE D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 644 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER D 645 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D 651 " --> pdb=" O THR D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 672 Processing helix chain 'D' and resid 689 through 699 removed outlier: 4.451A pdb=" N ARG D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 724 removed outlier: 3.945A pdb=" N ASP D 716 " --> pdb=" O ARG D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.603A pdb=" N ARG D 742 " --> pdb=" O TYR D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.656A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 4.609A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 845 removed outlier: 4.061A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR D 823 " --> pdb=" O ALA D 819 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.608A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 184 through 186 No H-bonds generated for 'chain 'H' and resid 184 through 186' Processing helix chain 'J' and resid 153 through 155 No H-bonds generated for 'chain 'J' and resid 153 through 155' Processing helix chain 'J' and resid 184 through 186 No H-bonds generated for 'chain 'J' and resid 184 through 186' Processing helix chain 'K' and resid 185 through 190 Processing helix chain 'L' and resid 125 through 129 Processing helix chain 'L' and resid 185 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 64 removed outlier: 6.486A pdb=" N LYS A 25 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASN A 61 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N LEU A 91 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 165 removed outlier: 6.530A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 354 through 357 Processing sheet with id=AA4, first strand: chain 'A' and resid 366 through 367 Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 730 through 732 removed outlier: 3.626A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.803A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 124 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 198 through 203 removed outlier: 8.499A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.564A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU B 277 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 405 through 409 removed outlier: 6.841A pdb=" N LEU B 406 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TYR B 479 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE B 408 " --> pdb=" O TYR B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 417 through 420 removed outlier: 3.754A pdb=" N LYS B 455 " --> pdb=" O CYS B 436 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS B 457 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 523 through 525 Processing sheet with id=AB3, first strand: chain 'B' and resid 534 through 536 removed outlier: 3.639A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AB5, first strand: chain 'C' and resid 58 through 65 removed outlier: 6.090A pdb=" N LYS C 25 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN C 61 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 165 through 167 removed outlier: 4.183A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 267 through 268 removed outlier: 4.480A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 401 through 402 removed outlier: 3.818A pdb=" N THR C 402 " --> pdb=" O HIS C 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.616A pdb=" N VAL C 451 " --> pdb=" O GLY C 438 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC2, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.276A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 39 through 41 removed outlier: 6.456A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 124 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE D 99 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 168 through 172 removed outlier: 8.764A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 257 through 258 removed outlier: 3.802A pdb=" N VAL D 280 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS D 380 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AC7, first strand: chain 'D' and resid 409 through 410 removed outlier: 4.040A pdb=" N THR D 410 " --> pdb=" O TYR D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 417 through 420 Processing sheet with id=AC9, first strand: chain 'D' and resid 524 through 525 removed outlier: 3.924A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 766 " --> pdb=" O ASP D 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 530 through 531 removed outlier: 4.125A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 535 through 536 removed outlier: 5.970A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.525A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 19 through 23 Processing sheet with id=AD5, first strand: chain 'H' and resid 122 through 126 removed outlier: 6.642A pdb=" N TYR H 173 " --> pdb=" O ASP H 141 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 122 through 126 removed outlier: 6.642A pdb=" N TYR H 173 " --> pdb=" O ASP H 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 148 through 151 removed outlier: 4.488A pdb=" N TYR H 191 " --> pdb=" O VAL H 208 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.529A pdb=" N MET J 93 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN J 39 " --> pdb=" O MET J 93 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 49 through 51 Processing sheet with id=AE2, first strand: chain 'J' and resid 122 through 126 removed outlier: 6.340A pdb=" N TYR J 173 " --> pdb=" O ASP J 141 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 122 through 126 removed outlier: 6.340A pdb=" N TYR J 173 " --> pdb=" O ASP J 141 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 147 through 151 removed outlier: 4.361A pdb=" N TYR J 191 " --> pdb=" O VAL J 208 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 64 through 65 removed outlier: 3.980A pdb=" N SER K 65 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR K 72 " --> pdb=" O SER K 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 89 through 90 removed outlier: 3.699A pdb=" N THR K 99 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 116 through 120 removed outlier: 6.388A pdb=" N TYR K 175 " --> pdb=" O ASN K 140 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 147 through 152 Processing sheet with id=AE9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AF1, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.662A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 62 through 65 removed outlier: 3.907A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.146A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 147 through 152 1133 hydrogen bonds defined for protein. 3237 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: 12.25 Time building geometry restraints manager: 8.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.24: 4263 1.24 - 1.54: 24563 1.54 - 1.84: 428 1.84 - 2.14: 2 2.14 - 2.43: 2 Bond restraints: 29258 Sorted by residual: bond pdb=" N PRO D 547 " pdb=" CD PRO D 547 " ideal model delta sigma weight residual 1.473 2.413 -0.940 1.40e-02 5.10e+03 4.50e+03 bond pdb=" CB PRO A 447 " pdb=" CG PRO A 447 " ideal model delta sigma weight residual 1.492 2.432 -0.940 5.00e-02 4.00e+02 3.53e+02 bond pdb=" CG PRO A 447 " pdb=" CD PRO A 447 " ideal model delta sigma weight residual 1.503 0.948 0.555 3.40e-02 8.65e+02 2.66e+02 bond pdb=" C SER A 446 " pdb=" N PRO A 447 " ideal model delta sigma weight residual 1.334 1.709 -0.375 2.34e-02 1.83e+03 2.57e+02 bond pdb=" N PRO A 447 " pdb=" CA PRO A 447 " ideal model delta sigma weight residual 1.469 1.314 0.155 1.28e-02 6.10e+03 1.47e+02 ... (remaining 29253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 39986 21.21 - 42.43: 4 42.43 - 63.64: 2 63.64 - 84.85: 0 84.85 - 106.07: 1 Bond angle restraints: 39993 Sorted by residual: angle pdb=" CB PRO A 447 " pdb=" CG PRO A 447 " pdb=" CD PRO A 447 " ideal model delta sigma weight residual 106.10 0.03 106.07 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO D 547 " pdb=" N PRO D 547 " pdb=" CD PRO D 547 " ideal model delta sigma weight residual 112.00 67.89 44.11 1.40e+00 5.10e-01 9.92e+02 angle pdb=" CA PRO A 447 " pdb=" N PRO A 447 " pdb=" CD PRO A 447 " ideal model delta sigma weight residual 112.00 80.83 31.17 1.40e+00 5.10e-01 4.96e+02 angle pdb=" N PRO D 547 " pdb=" CD PRO D 547 " pdb=" CG PRO D 547 " ideal model delta sigma weight residual 103.20 73.84 29.36 1.50e+00 4.44e-01 3.83e+02 angle pdb=" C SER A 446 " pdb=" N PRO A 447 " pdb=" CA PRO A 447 " ideal model delta sigma weight residual 119.84 100.37 19.47 1.25e+00 6.40e-01 2.43e+02 ... (remaining 39988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.25: 15286 20.25 - 40.50: 1617 40.50 - 60.75: 277 60.75 - 81.01: 38 81.01 - 101.26: 13 Dihedral angle restraints: 17231 sinusoidal: 5597 harmonic: 11634 Sorted by residual: dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 455 " pdb=" CB CYS A 455 " ideal model delta sinusoidal sigma weight residual 93.00 172.60 -79.60 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 308 " pdb=" CB CYS A 308 " ideal model delta sinusoidal sigma weight residual 93.00 14.22 78.78 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 308 " pdb=" CB CYS C 308 " ideal model delta sinusoidal sigma weight residual -86.00 -14.72 -71.28 1 1.00e+01 1.00e-02 6.52e+01 ... (remaining 17228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4445 0.096 - 0.191: 221 0.191 - 0.287: 6 0.287 - 0.383: 1 0.383 - 0.479: 1 Chirality restraints: 4674 Sorted by residual: chirality pdb=" CA PRO A 447 " pdb=" N PRO A 447 " pdb=" C PRO A 447 " pdb=" CB PRO A 447 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CG LEU B 112 " pdb=" CB LEU B 112 " pdb=" CD1 LEU B 112 " pdb=" CD2 LEU B 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA SER A 446 " pdb=" N SER A 446 " pdb=" C SER A 446 " pdb=" CB SER A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4671 not shown) Planarity restraints: 5152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 817 " 0.017 2.00e-02 2.50e+03 4.04e-02 2.86e+01 pdb=" CG PHE A 817 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE A 817 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 817 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE A 817 " -0.068 2.00e-02 2.50e+03 pdb=" CE2 PHE A 817 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 817 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 618 " -0.081 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO B 619 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO B 619 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 619 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 546 " -0.105 5.00e-02 4.00e+02 1.07e-01 1.85e+01 pdb=" N PRO D 547 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO D 547 " -0.007 5.00e-02 4.00e+02 pdb=" CD PRO D 547 " -0.064 5.00e-02 4.00e+02 ... (remaining 5149 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 343 2.62 - 3.19: 25822 3.19 - 3.76: 43477 3.76 - 4.33: 53432 4.33 - 4.90: 88083 Nonbonded interactions: 211157 Sorted by model distance: nonbonded pdb=" C PRO D 547 " pdb=" CD PRO D 547 " model vdw 2.047 2.936 nonbonded pdb=" OH TYR A 109 " pdb=" O GLN B 110 " model vdw 2.087 3.040 nonbonded pdb=" OE2 GLU K 197 " pdb=" OG1 THR K 199 " model vdw 2.090 3.040 nonbonded pdb=" O ASP C 343 " pdb=" OD1 ASP C 343 " model vdw 2.099 3.040 nonbonded pdb=" N GLU B 790 " pdb=" OE1 GLU B 790 " model vdw 2.108 3.120 ... (remaining 211152 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 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 36 or (resid 37 and (name N or name CA or name C or name \ O or name CB )) or resid 38 or (resid 39 and (name N or name CA or name C or nam \ e O or name CB )) or resid 40 through 43 or (resid 44 through 45 and (name N or \ name CA or name C or name O or name CB )) or resid 46 through 72 or (resid 73 an \ d (name N or name CA or name C or name O or name CB )) or resid 74 through 75 or \ (resid 76 and (name N or name CA or name C or name O or name CB )) or resid 77 \ through 79 or (resid 80 and (name N or name CA or name C or name O or name CB )) \ or resid 81 through 99 or (resid 100 and (name N or name CA or name C or name O \ or name CB )) or resid 101 through 102 or (resid 103 and (name N or name CA or \ name C or name O or name CB )) or resid 104 through 152 or (resid 153 and (name \ N or name CA or name C or name O or name CB )) or resid 154 through 177 or (resi \ d 178 and (name N or name CA or name C or name O or name CB )) or resid 179 thro \ ugh 180 or (resid 181 and (name N or name CA or name C or name O or name CB )) o \ r resid 182 through 186 or (resid 187 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 through 197 or (resid 198 and (name N or \ name CA or name C or name O or name CB )) or resid 199 through 214 or (resid 21 \ 5 through 216 and (name N or name CA or name C or name O or name CB )) or resid \ 217 through 224 or (resid 225 through 226 and (name N or name CA or name C or na \ me O or name CB )) or resid 227 through 293 or (resid 294 and (name N or name CA \ or name C or name O or name CB )) or resid 295 through 296 or (resid 297 throug \ h 299 and (name N or name CA or name C or name O or name CB )) or resid 300 thro \ ugh 315 or (resid 316 and (name N or name CA or name C or name O or name CB )) o \ r resid 317 through 328 or (resid 329 and (name N or name CA or name C or name O \ or name CB )) or resid 330 through 384 or (resid 385 and (name N or name CA or \ name C or name O or name CB )) or resid 386 through 393 or (resid 394 through 39 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 398 or (resi \ d 399 and (name N or name CA or name C or name O or name CB )) or resid 400 thro \ ugh 413 or (resid 414 through 417 and (name N or name CA or name C or name O or \ name CB )) or resid 418 or (resid 419 and (name N or name CA or name C or name O \ or name CB )) or resid 420 through 425 or (resid 426 through 427 and (name N or \ name CA or name C or name O or name CB )) or resid 428 through 431 or (resid 43 \ 2 through 433 and (name N or name CA or name C or name O or name CB )) or resid \ 434 through 448 or (resid 449 and (name N or name CA or name C or name O or name \ CB )) or resid 450 through 460 or (resid 461 and (name N or name CA or name C o \ r name O or name CB )) or resid 462 through 464 or (resid 465 and (name N or nam \ e CA or name C or name O or name CB )) or resid 466 through 467 or (resid 468 an \ d (name N or name CA or name C or name O or name CB )) or resid 469 through 485 \ or (resid 486 through 492 and (name N or name CA or name C or name O or name CB \ )) or resid 493 or (resid 494 through 497 and (name N or name CA or name C or na \ me O or name CB )) or resid 498 through 503 or (resid 504 and (name N or name CA \ or name C or name O or name CB )) or resid 505 through 521 or (resid 522 and (n \ ame N or name CA or name C or name O or name CB )) or resid 523 through 527 or ( \ resid 528 and (name N or name CA or name C or name O or name CB )) or resid 529 \ through 541 or (resid 542 through 545 and (name N or name CA or name C or name O \ or name CB )) or resid 546 through 547 or (resid 548 through 549 and (name N or \ name CA or name C or name O or name CB )) or resid 550 or (resid 551 through 55 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 553 through \ 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) or re \ sid 569 through 571 or (resid 572 and (name N or name CA or name C or name O or \ name CB )) or resid 573 through 580 or (resid 581 through 584 and (name N or nam \ e CA or name C or name O or name CB )) or resid 602 through 603 or (resid 604 an \ d (name N or name CA or name C or name O or name CB )) or resid 605 through 618 \ or (resid 619 and (name N or name CA or name C or name O or name CB )) or resid \ 620 through 633 or (resid 634 and (name N or name CA or name C or name O or name \ CB )) or resid 635 through 656 or (resid 657 and (name N or name CA or name C o \ r name O or name CB )) or resid 658 through 666 or (resid 667 through 669 and (n \ ame N or name CA or name C or name O or name CB )) or resid 670 or (resid 671 th \ rough 672 and (name N or name CA or name C or name O or name CB )) or resid 673 \ through 676 or (resid 677 through 679 and (name N or name CA or name C or name O \ or name CB )) or resid 680 through 684 or (resid 685 through 686 and (name N or \ name CA or name C or name O or name CB )) or resid 687 through 689 or (resid 69 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 691 through \ 696 or (resid 697 and (name N or name CA or name C or name O or name CB )) or re \ sid 698 or (resid 699 through 709 and (name N or name CA or name C or name O or \ name CB )) or resid 710 or (resid 711 through 718 and (name N or name CA or name \ C or name O or name CB )) or resid 719 through 731 or (resid 732 and (name N or \ name CA or name C or name O or name CB )) or resid 733 through 747 or (resid 74 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 749 through \ 764 or (resid 765 and (name N or name CA or name C or name O or name CB )) or re \ sid 766 through 768 or (resid 769 and (name N or name CA or name C or name O or \ name CB )) or resid 770 through 792 or (resid 793 through 794 and (name N or nam \ e CA or name C or name O or name CB )) or resid 795 or (resid 796 through 797 an \ d (name N or name CA or name C or name O or name CB )) or resid 798 or (resid 79 \ 9 through 804 and (name N or name CA or name C or name O or name CB )) or resid \ 805 through 810 or (resid 811 through 814 and (name N or name CA or name C or na \ me O or name CB )) or resid 815 through 819 or (resid 820 through 821 and (name \ N or name CA or name C or name O or name CB )) or resid 822 through 828 or (resi \ d 829 through 841 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 23 through 386 or (resid 387 and (name N or name CA or nam \ e C or name O or name CB )) or resid 388 through 414 or (resid 415 through 417 a \ nd (name N or name CA or name C or name O or name CB )) or resid 418 through 482 \ or (resid 483 and (name N or name CA or name C or name O or name CB )) or resid \ 484 through 542 or (resid 543 through 545 and (name N or name CA or name C or n \ ame O or name CB )) or resid 546 through 551 or (resid 552 and (name N or name C \ A or name C or name O or name CB )) or resid 553 through 555 or (resid 556 and ( \ name N or name CA or name C or name O or name CB )) or resid 557 through 576 or \ (resid 577 through 578 and (name N or name CA or name C or name O or name CB )) \ or resid 579 through 583 or (resid 584 and (name N or name CA or name C or name \ O or name CB )) or resid 602 through 606 or (resid 607 and (name N or name CA or \ name C or name O or name CB )) or resid 608 through 624 or (resid 625 through 6 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 627 through \ 667 or (resid 668 through 669 and (name N or name CA or name C or name O or nam \ e CB )) or resid 670 through 694 or (resid 695 and (name N or name CA or name C \ or name O or name CB )) or resid 696 through 704 or (resid 705 through 709 and ( \ name N or name CA or name C or name O or name CB )) or resid 710 through 715 or \ (resid 716 through 718 and (name N or name CA or name C or name O or name CB )) \ or resid 719 through 736 or (resid 737 and (name N or name CA or name C or name \ O or name CB )) or resid 738 or (resid 739 through 740 and (name N or name CA or \ name C or name O or name CB )) or resid 741 through 743 or (resid 744 through 7 \ 45 and (name N or name CA or name C or name O or name CB )) or resid 746 through \ 785 or (resid 786 and (name N or name CA or name C or name O or name CB )) or r \ esid 787 through 799 or (resid 800 through 804 and (name N or name CA or name C \ or name O or name CB )) or resid 805 through 841)) } ncs_group { reference = (chain 'B' and (resid 31 through 33 or (resid 34 through 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 41 or (resid 42 and (na \ me N or name CA or name C or name O or name CB )) or resid 43 through 57 or (res \ id 58 and (name N or name CA or name C or name O or name CB )) or resid 59 throu \ gh 61 or (resid 62 through 65 and (name N or name CA or name C or name O or name \ CB )) or resid 66 or (resid 67 through 77 and (name N or name CA or name C or n \ ame O or name CB )) or resid 78 through 80 or (resid 81 and (name N or name CA o \ r name C or name O or name CB )) or resid 82 through 86 or (resid 87 and (name N \ or name CA or name C or name O or name CB )) or resid 88 through 90 or (resid 9 \ 1 through 92 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 3 through 102 or (resid 103 through 107 and (name N or name CA or name C or name \ O or name CB )) or resid 108 through 109 or (resid 110 and (name N or name CA o \ r name C or name O or name CB )) or resid 111 through 115 or (resid 116 through \ 117 and (name N or name CA or name C or name O or name CB )) or resid 118 throug \ h 122 or (resid 123 and (name N or name CA or name C or name O or name CB )) or \ resid 124 through 131 or (resid 132 and (name N or name CA or name C or name O o \ r name CB )) or resid 133 through 138 or (resid 139 and (name N or name CA or na \ me C or name O or name CB )) or resid 140 through 150 or (resid 151 and (name N \ or name CA or name C or name O or name CB )) or resid 152 through 159 or (resid \ 160 through 162 and (name N or name CA or name C or name O or name CB )) or resi \ d 163 or (resid 164 through 165 and (name N or name CA or name C or name O or na \ me CB )) or resid 166 or (resid 167 and (name N or name CA or name C or name O o \ r name CB )) or resid 168 or (resid 169 and (name N or name CA or name C or name \ O or name CB )) or resid 170 or (resid 171 through 176 and (name N or name CA o \ r name C or name O or name CB )) or resid 177 through 178 or (resid 179 through \ 181 and (name N or name CA or name C or name O or name CB )) or resid 182 or (re \ sid 183 through 185 and (name N or name CA or name C or name O or name CB )) or \ resid 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) \ or resid 188 through 189 or (resid 190 through 192 and (name N or name CA or na \ me C or name O or name CB )) or resid 193 or (resid 194 and (name N or name CA o \ r name C or name O or name CB )) or resid 195 through 198 or (resid 199 through \ 211 and (name N or name CA or name C or name O or name CB )) or resid 212 or (re \ sid 213 and (name N or name CA or name C or name O or name CB )) or resid 214 th \ rough 215 or (resid 216 through 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 or (resid 220 through 224 and (name N or name CA or na \ me C or name O or name CB )) or resid 225 through 230 or (resid 231 and (name N \ or name CA or name C or name O or name CB )) or resid 232 or (resid 233 through \ 234 and (name N or name CA or name C or name O or name CB )) or resid 235 or (re \ sid 236 through 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 246 or (resid 247 and (name N or name CA or name C or name O o \ r name CB )) or resid 248 or (resid 249 through 250 and (name N or name CA or na \ me C or name O or name CB )) or resid 251 through 260 or (resid 261 and (name N \ or name CA or name C or name O or name CB )) or resid 262 through 264 or (resid \ 265 through 267 and (name N or name CA or name C or name O or name CB )) or resi \ d 268 or (resid 269 and (name N or name CA or name C or name O or name CB )) or \ resid 270 through 272 or (resid 273 and (name N or name CA or name C or name O o \ r name CB )) or resid 274 through 284 or (resid 285 through 286 and (name N or n \ ame CA or name C or name O or name CB )) or resid 287 through 299 or (resid 300 \ and (name N or name CA or name C or name O or name CB )) or resid 301 through 30 \ 5 or (resid 306 through 308 and (name N or name CA or name C or name O or name C \ B )) or resid 309 or (resid 310 through 311 and (name N or name CA or name C or \ name O or name CB )) or resid 312 through 313 or (resid 314 and (name N or name \ CA or name C or name O or name CB )) or resid 315 through 318 or (resid 319 thro \ ugh 320 and (name N or name CA or name C or name O or name CB )) or resid 321 th \ rough 333 or (resid 334 through 335 and (name N or name CA or name C or name O o \ r name CB )) or resid 336 through 337 or (resid 338 and (name N or name CA or na \ me C or name O or name CB )) or resid 339 through 341 or (resid 342 and (name N \ or name CA or name C or name O or name CB )) or resid 343 or (resid 344 through \ 345 and (name N or name CA or name C or name O or name CB )) or resid 346 throug \ h 347 or (resid 348 and (name N or name CA or name C or name O or name CB )) or \ resid 349 through 352 or (resid 353 through 354 and (name N or name CA or name C \ or name O or name CB )) or resid 355 or (resid 356 and (name N or name CA or na \ me C or name O or name CB )) or resid 357 or (resid 358 and (name N or name CA o \ r name C or name O or name CB )) or resid 359 through 366 or (resid 367 through \ 372 and (name N or name CA or name C or name O or name CB )) or resid 373 throug \ h 374 or (resid 375 and (name N or name CA or name C or name O or name CB )) or \ resid 376 through 379 or (resid 380 through 382 and (name N or name CA or name C \ or name O or name CB )) or resid 383 through 390 or (resid 391 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 403 through 404 and (name N o \ r name CA or name C or name O or name CB )) or resid 405 through 419 or (resid 4 \ 20 and (name N or name CA or name C or name O or name CB )) or resid 421 or (res \ id 422 through 423 and (name N or name CA or name C or name O or name CB )) or r \ esid 424 through 431 or (resid 432 through 434 and (name N or name CA or name C \ or name O or name CB )) or resid 435 through 438 or (resid 439 through 449 and ( \ name N or name CA or name C or name O or name CB )) or resid 450 through 451 or \ (resid 452 through 455 and (name N or name CA or name C or name O or name CB )) \ or resid 456 through 462 or (resid 463 and (name N or name CA or name C or name \ O or name CB )) or resid 464 through 476 or (resid 477 and (name N or name CA or \ name C or name O or name CB )) or resid 478 through 480 or (resid 481 through 4 \ 82 and (name N or name CA or name C or name O or name CB )) or resid 483 through \ 492 or (resid 493 and (name N or name CA or name C or name O or name CB )) or r \ esid 494 through 496 or (resid 497 and (name N or name CA or name C or name O or \ name CB )) or resid 498 through 499 or (resid 500 through 506 and (name N or na \ me CA or name C or name O or name CB )) or resid 507 through 515 or resid 517 th \ rough 523 or (resid 524 and (name N or name CA or name C or name O or name CB )) \ or resid 525 through 535 or (resid 536 through 538 and (name N or name CA or na \ me C or name O or name CB )) or resid 539 or (resid 540 and (name N or name CA o \ r name C or name O or name CB )) or resid 541 or (resid 542 and (name N or name \ CA or name C or name O or name CB )) or resid 543 through 549 or (resid 550 thro \ ugh 552 and (name N or name CA or name C or name O or name CB )) or resid 553 th \ rough 556 or (resid 557 and (name N or name CA or name C or name O or name CB )) \ or resid 558 through 560 or (resid 561 and (name N or name CA or name C or name \ O or name CB )) or resid 562 through 573 or (resid 574 through 579 and (name N \ or name CA or name C or name O or name CB )) or resid 599 through 600 or (resid \ 601 through 602 and (name N or name CA or name C or name O or name CB )) or resi \ d 603 or (resid 604 through 606 and (name N or name CA or name C or name O or na \ me CB )) or resid 607 through 617 or (resid 618 and (name N or name CA or name C \ or name O or name CB )) or resid 619 through 620 or (resid 621 and (name N or n \ ame CA or name C or name O or name CB )) or resid 622 through 623 or (resid 624 \ and (name N or name CA or name C or name O or name CB )) or resid 625 through 66 \ 2 or (resid 663 and (name N or name CA or name C or name O or name CB )) or resi \ d 664 through 665 or (resid 666 and (name N or name CA or name C or name O or na \ me CB )) or resid 667 through 669 or (resid 670 and (name N or name CA or name C \ or name O or name CB )) or resid 671 through 684 or (resid 685 through 686 and \ (name N or name CA or name C or name O or name CB )) or resid 687 through 691 or \ (resid 692 and (name N or name CA or name C or name O or name CB )) or resid 69 \ 3 through 695 or (resid 696 and (name N or name CA or name C or name O or name C \ B )) or resid 697 through 700 or (resid 701 through 706 and (name N or name CA o \ r name C or name O or name CB )) or (resid 707 through 712 and (name N or name C \ A or name C or name O or name CB )) or resid 713 through 747 or (resid 748 throu \ gh 749 and (name N or name CA or name C or name O or name CB )) or resid 750 thr \ ough 754 or (resid 755 and (name N or name CA or name C or name O or name CB )) \ or resid 756 through 774 or (resid 775 and (name N or name CA or name C or name \ O or name CB )) or resid 776 or (resid 777 and (name N or name CA or name C or n \ ame O or name CB )) or resid 778 through 785 or (resid 786 and (name N or name C \ A or name C or name O or name CB )) or resid 787 or (resid 788 and (name N or na \ me CA or name C or name O or name CB )) or resid 789 or (resid 790 through 791 a \ nd (name N or name CA or name C or name O or name CB )) or resid 792 through 794 \ or (resid 795 and (name N or name CA or name C or name O or name CB )) or resid \ 796 through 811 or (resid 812 and (name N or name CA or name C or name O or nam \ e CB )) or resid 813 through 817 or (resid 818 through 819 and (name N or name C \ A or name C or name O or name CB )) or resid 820 through 835 or (resid 836 and ( \ name N or name CA or name C or name O or name CB )) or resid 837 through 839 or \ (resid 840 through 845 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'D' and (resid 31 through 50 or (resid 51 through 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 271 or (resid 272 throu \ gh 273 and (name N or name CA or name C or name O or name CB )) or resid 274 thr \ ough 340 or (resid 341 through 342 and (name N or name CA or name C or name O or \ name CB )) or resid 343 through 344 or (resid 345 and (name N or name CA or nam \ e C or name O or name CB )) or resid 346 through 411 or (resid 412 and (name N o \ r name CA or name C or name O or name CB )) or resid 413 through 422 or (resid 4 \ 23 and (name N or name CA or name C or name O or name CB )) or resid 424 through \ 531 or (resid 532 and (name N or name CA or name C or name O or name CB )) or r \ esid 533 through 545 or (resid 546 and (name N or name CA or name C or name O or \ name CB )) or resid 547 through 559 or (resid 560 through 561 and (name N or na \ me CA or name C or name O or name CB )) or resid 562 or (resid 563 through 564 a \ nd (name N or name CA or name C or name O or name CB )) or resid 565 through 567 \ or (resid 568 and (name N or name CA or name C or name O or name CB )) or resid \ 569 or (resid 570 through 571 and (name N or name CA or name C or name O or nam \ e CB )) or resid 572 through 601 or (resid 602 and (name N or name CA or name C \ or name O or name CB )) or (resid 603 through 606 and (name N or name CA or name \ C or name O or name CB )) or resid 607 through 661 or (resid 662 through 663 an \ d (name N or name CA or name C or name O or name CB )) or resid 664 through 668 \ or (resid 669 through 670 and (name N or name CA or name C or name O or name CB \ )) or resid 671 through 677 or (resid 678 and (name N or name CA or name C or na \ me O or name CB )) or resid 679 through 704 or (resid 705 through 706 and (name \ N or name CA or name C or name O or name CB )) or resid 707 or (resid 708 throug \ h 712 and (name N or name CA or name C or name O or name CB )) or resid 713 thro \ ugh 714 or (resid 715 through 717 and (name N or name CA or name C or name O or \ name CB )) or resid 718 through 722 or (resid 723 and (name N or name CA or name \ C or name O or name CB )) or resid 724 through 731 or (resid 732 through 734 an \ d (name N or name CA or name C or name O or name CB )) or resid 735 through 741 \ or (resid 742 through 744 and (name N or name CA or name C or name O or name CB \ )) or resid 745 through 766 or (resid 767 through 769 and (name N or name CA or \ name C or name O or name CB )) or resid 770 through 790 or (resid 791 and (name \ N or name CA or name C or name O or name CB )) or resid 792 or (resid 793 throug \ h 795 and (name N or name CA or name C or name O or name CB )) or resid 796 thro \ ugh 797 or (resid 798 and (name N or name CA or name C or name O or name CB )) o \ r (resid 799 through 812 and (name N or name CA or name C or name O or name CB ) \ ) or resid 813 through 815 or (resid 816 and (name N or name CA or name C or nam \ e O or name CB )) or resid 817 through 822 or (resid 823 through 824 and (name N \ or name CA or name C or name O or name CB )) or resid 825 through 830 or (resid \ 831 and (name N or name CA or name C or name O or name CB )) or resid 832 throu \ gh 834 or (resid 835 through 836 and (name N or name CA or name C or name O or n \ ame CB )) or resid 837 through 840 or (resid 841 through 845 and (name N or name \ CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'H' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 19 or (resid 20 through 21 and (nam \ e N or name CA or name C or name O or name CB )) or resid 22 or (resid 23 throug \ h 25 and (name N or name CA or name C or name O or name CB )) or resid 26 throug \ h 27 or (resid 28 and (name N or name CA or name C or name O or name CB )) or re \ sid 29 through 38 or (resid 39 through 40 and (name N or name CA or name C or na \ me O or name CB )) or resid 41 through 64 or (resid 65 and (name N or name CA or \ name C or name O or name CB )) or resid 66 or (resid 67 through 70 and (name N \ or name CA or name C or name O or name CB )) or resid 71 through 77 or (resid 78 \ through 79 and (name N or name CA or name C or name O or name CB )) or resid 80 \ or (resid 81 through 82 and (name N or name CA or name C or name O or name CB ) \ ) or resid 83 through 88 or (resid 89 through 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 through 211)) selection = (chain 'J' and (resid 2 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 211)) } ncs_group { reference = (chain 'K' and ((resid 1 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 10 or (resid 11 through 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 41 or (resid 42 through 4 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 44 through 1 \ 01 or (resid 102 and (name N or name CA or name C or name O or name CB )) or (re \ sid 103 through 109 and (name N or name CA or name C or name O or name CB )) or \ resid 110 through 215)) selection = (chain 'L' and ((resid 1 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 21 or (resid 22 and (name N or name CA or name C \ or name O or name CB )) or resid 23 through 26 or (resid 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 through 32 or (resid 33 through \ 34 and (name N or name CA or name C or name O or name CB )) or resid 35 through \ 37 or (resid 38 and (name N or name CA or name C or name O or name CB )) or res \ id 39 through 46 or (resid 47 and (name N or name CA or name C or name O or name \ CB )) or resid 48 through 52 or (resid 53 through 56 and (name N or name CA or \ name C or name O or name CB )) or resid 57 through 61 or (resid 62 and (name N o \ r name CA or name C or name O or name CB )) or resid 63 through 66 or (resid 67 \ and (name N or name CA or name C or name O or name CB )) or (resid 68 through 71 \ and (name N or name CA or name C or name O or name CB )) or resid 72 through 73 \ or (resid 74 through 80 and (name N or name CA or name C or name O or name CB ) \ ) or resid 81 through 91 or (resid 92 and (name N or name CA or name C or name O \ or name CB )) or resid 93 through 215)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.040 Extract box with map and model: 1.130 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 69.000 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 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 : 0.010 0.940 29280 Z= 0.472 Angle : 0.969 106.068 40037 Z= 0.464 Chirality : 0.044 0.479 4674 Planarity : 0.005 0.118 5152 Dihedral : 16.679 101.257 9661 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.42 % Favored : 90.28 % Rotamer: Outliers : 0.19 % Allowed : 35.47 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.14), residues: 3992 helix: 0.77 (0.15), residues: 1194 sheet: -1.38 (0.20), residues: 744 loop : -2.58 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 56 HIS 0.002 0.000 HIS K 200 PHE 0.069 0.001 PHE A 817 TYR 0.028 0.001 TYR C 144 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.16880 ( 1103) hydrogen bonds : angle 6.69952 ( 3237) SS BOND : bond 0.02175 ( 22) SS BOND : angle 1.99275 ( 44) covalent geometry : bond 0.00976 (29258) covalent geometry : angle 0.96699 (39993) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 278 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 282 average time/residue: 0.3339 time to fit residues: 159.1165 Evaluate side-chains 279 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 277 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 30.0000 chunk 303 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 204 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 313 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 233 optimal weight: 0.2980 chunk 363 optimal weight: 40.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 73 GLN A 161 ASN A 162 HIS A 727 HIS B 145 GLN B 152 GLN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN C 38 HIS C 147 GLN C 162 HIS C 357 GLN C 556 ASN C 705 HIS D 127 HIS D 359 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 ASN K 162 GLN L 168 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.157349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.136603 restraints weight = 94086.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.134411 restraints weight = 128699.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.131760 restraints weight = 122250.829| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 29280 Z= 0.344 Angle : 0.844 11.216 40037 Z= 0.443 Chirality : 0.050 0.231 4674 Planarity : 0.006 0.099 5152 Dihedral : 5.570 34.235 4240 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.78 % Favored : 86.90 % Rotamer: Outliers : 0.68 % Allowed : 7.58 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.29 (0.13), residues: 3992 helix: 0.33 (0.15), residues: 1237 sheet: -1.51 (0.20), residues: 736 loop : -2.82 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP L 94 HIS 0.024 0.002 HIS A 780 PHE 0.058 0.003 PHE A 533 TYR 0.045 0.003 TYR A 109 ARG 0.010 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.06078 ( 1103) hydrogen bonds : angle 5.76879 ( 3237) SS BOND : bond 0.00552 ( 22) SS BOND : angle 1.56614 ( 44) covalent geometry : bond 0.00811 (29258) covalent geometry : angle 0.84313 (39993) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 341 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TRP cc_start: 0.7763 (p-90) cc_final: 0.7534 (p-90) REVERT: A 161 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7730 (t0) REVERT: A 248 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8176 (mt) REVERT: C 322 LYS cc_start: 0.5323 (mmtt) cc_final: 0.5071 (mptt) REVERT: C 641 MET cc_start: 0.9205 (tmm) cc_final: 0.8631 (tmm) REVERT: D 134 MET cc_start: 0.5357 (tmm) cc_final: 0.5092 (tmm) REVERT: K 102 GLN cc_start: 0.1579 (pm20) cc_final: 0.0350 (tp40) outliers start: 18 outliers final: 11 residues processed: 358 average time/residue: 0.3706 time to fit residues: 214.5380 Evaluate side-chains 284 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 271 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 361 optimal weight: 50.0000 chunk 160 optimal weight: 8.9990 chunk 283 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 337 optimal weight: 8.9990 chunk 398 optimal weight: 50.0000 chunk 151 optimal weight: 1.9990 chunk 331 optimal weight: 50.0000 chunk 225 optimal weight: 0.2980 chunk 338 optimal weight: 50.0000 chunk 9 optimal weight: 2.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 162 HIS A 257 ASN B 152 GLN B 192 ASN ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN L 200 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.151600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.129898 restraints weight = 89528.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.127533 restraints weight = 136156.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.125765 restraints weight = 110446.188| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 29280 Z= 0.225 Angle : 0.712 12.114 40037 Z= 0.370 Chirality : 0.047 0.223 4674 Planarity : 0.005 0.098 5152 Dihedral : 5.286 40.013 4240 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.92 % Favored : 88.78 % Rotamer: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.15 (0.13), residues: 3992 helix: 0.59 (0.15), residues: 1235 sheet: -1.48 (0.20), residues: 745 loop : -2.82 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 607 HIS 0.008 0.001 HIS A 780 PHE 0.035 0.002 PHE B 241 TYR 0.040 0.002 TYR A 109 ARG 0.012 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 1103) hydrogen bonds : angle 5.22094 ( 3237) SS BOND : bond 0.00516 ( 22) SS BOND : angle 1.63719 ( 44) covalent geometry : bond 0.00531 (29258) covalent geometry : angle 0.71062 (39993) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 329 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TRP cc_start: 0.7819 (p-90) cc_final: 0.7544 (p-90) REVERT: B 418 ILE cc_start: 0.7252 (pt) cc_final: 0.7047 (pt) REVERT: C 41 MET cc_start: 0.8339 (pmm) cc_final: 0.8034 (pmm) REVERT: C 322 LYS cc_start: 0.5313 (mmtt) cc_final: 0.5080 (mptt) REVERT: C 641 MET cc_start: 0.9231 (tmm) cc_final: 0.8577 (tmm) REVERT: D 134 MET cc_start: 0.5280 (tmm) cc_final: 0.5014 (tmm) REVERT: K 102 GLN cc_start: 0.1497 (pm20) cc_final: 0.1170 (tp40) REVERT: L 165 VAL cc_start: 0.4139 (t) cc_final: 0.3924 (t) outliers start: 2 outliers final: 1 residues processed: 331 average time/residue: 0.3559 time to fit residues: 194.0047 Evaluate side-chains 279 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 143 optimal weight: 1.9990 chunk 303 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 313 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 30.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS D 405 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.161963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.140688 restraints weight = 95787.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.139490 restraints weight = 141188.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.138034 restraints weight = 113161.189| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29280 Z= 0.125 Angle : 0.617 11.582 40037 Z= 0.319 Chirality : 0.044 0.221 4674 Planarity : 0.005 0.097 5152 Dihedral : 4.904 38.315 4240 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.97 % Favored : 89.75 % Rotamer: Outliers : 0.08 % Allowed : 2.57 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.81 (0.14), residues: 3992 helix: 0.97 (0.15), residues: 1243 sheet: -1.38 (0.20), residues: 755 loop : -2.66 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 796 HIS 0.007 0.001 HIS B 61 PHE 0.034 0.002 PHE B 241 TYR 0.031 0.001 TYR A 109 ARG 0.011 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 1103) hydrogen bonds : angle 4.74517 ( 3237) SS BOND : bond 0.00358 ( 22) SS BOND : angle 1.25280 ( 44) covalent geometry : bond 0.00287 (29258) covalent geometry : angle 0.61597 (39993) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TRP cc_start: 0.7689 (p-90) cc_final: 0.7405 (p-90) REVERT: A 125 MET cc_start: 0.8104 (tpp) cc_final: 0.7739 (mmt) REVERT: A 424 PHE cc_start: 0.7151 (m-80) cc_final: 0.6941 (m-80) REVERT: B 37 ILE cc_start: 0.8316 (tt) cc_final: 0.7947 (mt) REVERT: B 157 MET cc_start: 0.8063 (ptp) cc_final: 0.7817 (ptp) REVERT: C 41 MET cc_start: 0.8183 (pmm) cc_final: 0.7924 (pmm) REVERT: C 184 LEU cc_start: 0.8460 (pp) cc_final: 0.8066 (mt) REVERT: C 322 LYS cc_start: 0.5305 (mmtt) cc_final: 0.4966 (mptt) REVERT: C 641 MET cc_start: 0.9041 (tmm) cc_final: 0.8677 (tmm) REVERT: D 134 MET cc_start: 0.5193 (tmm) cc_final: 0.4958 (tmm) REVERT: K 102 GLN cc_start: 0.2128 (pm20) cc_final: 0.1516 (tp40) REVERT: K 125 GLU cc_start: 0.0555 (mt-10) cc_final: 0.0319 (pp20) REVERT: L 165 VAL cc_start: 0.4199 (t) cc_final: 0.3964 (t) outliers start: 2 outliers final: 2 residues processed: 350 average time/residue: 0.3610 time to fit residues: 209.0106 Evaluate side-chains 283 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 166 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 254 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 chunk 260 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS B 192 ASN ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 697 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.150490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.126738 restraints weight = 88395.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.125177 restraints weight = 130391.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.124012 restraints weight = 96483.536| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 29280 Z= 0.257 Angle : 0.729 11.664 40037 Z= 0.380 Chirality : 0.047 0.219 4674 Planarity : 0.005 0.099 5152 Dihedral : 5.265 37.661 4240 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.25 % Favored : 87.45 % Rotamer: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.03 (0.13), residues: 3992 helix: 0.67 (0.15), residues: 1237 sheet: -1.48 (0.19), residues: 757 loop : -2.71 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 796 HIS 0.008 0.001 HIS A 780 PHE 0.026 0.002 PHE C 533 TYR 0.029 0.002 TYR A 109 ARG 0.009 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.05176 ( 1103) hydrogen bonds : angle 5.08862 ( 3237) SS BOND : bond 0.00441 ( 22) SS BOND : angle 1.48899 ( 44) covalent geometry : bond 0.00606 (29258) covalent geometry : angle 0.72818 (39993) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TRP cc_start: 0.7918 (p-90) cc_final: 0.7491 (p-90) REVERT: B 565 MET cc_start: 0.7315 (mmm) cc_final: 0.7114 (mmm) REVERT: C 41 MET cc_start: 0.8210 (pmm) cc_final: 0.7900 (pmm) REVERT: C 322 LYS cc_start: 0.5565 (mmtt) cc_final: 0.4400 (mptt) REVERT: D 134 MET cc_start: 0.5372 (tmm) cc_final: 0.5131 (tmm) REVERT: K 102 GLN cc_start: 0.1851 (pm20) cc_final: 0.1297 (tp40) REVERT: L 165 VAL cc_start: 0.4300 (t) cc_final: 0.4036 (t) outliers start: 1 outliers final: 1 residues processed: 330 average time/residue: 0.3563 time to fit residues: 195.0123 Evaluate side-chains 274 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 9 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 257 optimal weight: 0.0170 chunk 70 optimal weight: 0.7980 chunk 310 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 192 optimal weight: 0.1980 chunk 372 optimal weight: 3.9990 chunk 328 optimal weight: 0.0040 chunk 102 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 overall best weight: 0.4030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN B 192 ASN C 50 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.155425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.130839 restraints weight = 85243.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.126429 restraints weight = 119188.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.123540 restraints weight = 113583.963| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29280 Z= 0.117 Angle : 0.621 11.896 40037 Z= 0.318 Chirality : 0.044 0.220 4674 Planarity : 0.005 0.098 5152 Dihedral : 4.835 38.601 4240 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.64 % Favored : 91.08 % Rotamer: Outliers : 0.04 % Allowed : 1.66 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.63 (0.14), residues: 3992 helix: 1.09 (0.15), residues: 1246 sheet: -1.37 (0.19), residues: 763 loop : -2.50 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 315 HIS 0.009 0.001 HIS C 780 PHE 0.029 0.002 PHE B 241 TYR 0.034 0.001 TYR D 731 ARG 0.007 0.000 ARG D 742 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 1103) hydrogen bonds : angle 4.54729 ( 3237) SS BOND : bond 0.00330 ( 22) SS BOND : angle 1.37529 ( 44) covalent geometry : bond 0.00260 (29258) covalent geometry : angle 0.61990 (39993) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TRP cc_start: 0.8065 (p-90) cc_final: 0.7640 (p-90) REVERT: B 157 MET cc_start: 0.8168 (ptp) cc_final: 0.7890 (ptp) REVERT: C 41 MET cc_start: 0.8609 (pmm) cc_final: 0.8185 (pmm) REVERT: C 119 LEU cc_start: 0.8130 (mm) cc_final: 0.7836 (mt) REVERT: C 322 LYS cc_start: 0.5432 (mmtt) cc_final: 0.5026 (mptt) REVERT: D 134 MET cc_start: 0.5211 (tmm) cc_final: 0.4946 (tmm) REVERT: D 532 THR cc_start: 0.9320 (p) cc_final: 0.9024 (t) REVERT: K 102 GLN cc_start: 0.2720 (pm20) cc_final: 0.2172 (tp40) REVERT: K 197 GLU cc_start: 0.5418 (tm-30) cc_final: 0.5034 (tm-30) REVERT: L 165 VAL cc_start: 0.4412 (t) cc_final: 0.4205 (t) outliers start: 1 outliers final: 0 residues processed: 347 average time/residue: 0.3596 time to fit residues: 206.5783 Evaluate side-chains 279 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 257 optimal weight: 30.0000 chunk 296 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 373 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 248 optimal weight: 0.0770 chunk 147 optimal weight: 0.9980 chunk 300 optimal weight: 40.0000 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.154440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.130197 restraints weight = 85608.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.126270 restraints weight = 121114.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.124405 restraints weight = 107300.140| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29280 Z= 0.123 Angle : 0.615 12.266 40037 Z= 0.314 Chirality : 0.044 0.218 4674 Planarity : 0.005 0.098 5152 Dihedral : 4.669 34.190 4240 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.84 % Favored : 89.88 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.56 (0.14), residues: 3992 helix: 1.20 (0.15), residues: 1238 sheet: -1.38 (0.19), residues: 783 loop : -2.45 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 315 HIS 0.008 0.001 HIS C 780 PHE 0.029 0.002 PHE B 241 TYR 0.039 0.001 TYR C 795 ARG 0.006 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 1103) hydrogen bonds : angle 4.45929 ( 3237) SS BOND : bond 0.00376 ( 22) SS BOND : angle 1.29999 ( 44) covalent geometry : bond 0.00288 (29258) covalent geometry : angle 0.61344 (39993) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 TRP cc_start: 0.8070 (p-90) cc_final: 0.7767 (p-90) REVERT: B 157 MET cc_start: 0.8161 (ptp) cc_final: 0.7907 (ptp) REVERT: C 41 MET cc_start: 0.8472 (pmm) cc_final: 0.8158 (pmm) REVERT: C 119 LEU cc_start: 0.8115 (mm) cc_final: 0.7776 (tp) REVERT: C 322 LYS cc_start: 0.5440 (mmtt) cc_final: 0.5020 (mptt) REVERT: C 819 ILE cc_start: 0.8346 (tp) cc_final: 0.7995 (tp) REVERT: D 134 MET cc_start: 0.5178 (tmm) cc_final: 0.4951 (tmm) REVERT: K 89 GLN cc_start: -0.0044 (pm20) cc_final: -0.0822 (pp30) REVERT: K 102 GLN cc_start: 0.2481 (pm20) cc_final: 0.2119 (tp40) REVERT: K 197 GLU cc_start: 0.5439 (tm-30) cc_final: 0.5140 (tm-30) REVERT: L 165 VAL cc_start: 0.4371 (t) cc_final: 0.4170 (t) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.3406 time to fit residues: 191.7216 Evaluate side-chains 282 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 359 optimal weight: 40.0000 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 240 optimal weight: 30.0000 chunk 141 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN ** K 200 HIS ** 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 = 0.4527 r_free = 0.4527 target = 0.162348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.141267 restraints weight = 95437.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.139710 restraints weight = 137522.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.137850 restraints weight = 111829.788| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29280 Z= 0.120 Angle : 0.611 13.192 40037 Z= 0.310 Chirality : 0.044 0.273 4674 Planarity : 0.005 0.098 5152 Dihedral : 4.624 45.746 4240 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.92 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3992 helix: 1.26 (0.15), residues: 1242 sheet: -1.33 (0.19), residues: 782 loop : -2.40 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 56 HIS 0.006 0.001 HIS B 61 PHE 0.024 0.001 PHE B 241 TYR 0.035 0.001 TYR C 795 ARG 0.007 0.000 ARG D 742 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 1103) hydrogen bonds : angle 4.38283 ( 3237) SS BOND : bond 0.00428 ( 22) SS BOND : angle 1.24417 ( 44) covalent geometry : bond 0.00279 (29258) covalent geometry : angle 0.61013 (39993) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ILE cc_start: 0.8394 (tt) cc_final: 0.7995 (mt) REVERT: B 157 MET cc_start: 0.8056 (ptp) cc_final: 0.7777 (ptp) REVERT: B 565 MET cc_start: 0.6856 (mmm) cc_final: 0.6640 (mmm) REVERT: C 119 LEU cc_start: 0.7148 (mm) cc_final: 0.6871 (mt) REVERT: C 184 LEU cc_start: 0.8380 (pp) cc_final: 0.8066 (mt) REVERT: C 322 LYS cc_start: 0.5350 (mmtt) cc_final: 0.4849 (mptt) REVERT: C 819 ILE cc_start: 0.8274 (tp) cc_final: 0.7902 (tp) REVERT: D 134 MET cc_start: 0.5394 (tmm) cc_final: 0.4845 (tmm) REVERT: K 89 GLN cc_start: -0.0656 (pm20) cc_final: -0.0918 (pp30) REVERT: K 197 GLU cc_start: 0.5803 (tm-30) cc_final: 0.5496 (tm-30) REVERT: L 165 VAL cc_start: 0.4234 (t) cc_final: 0.4021 (t) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.3558 time to fit residues: 199.0224 Evaluate side-chains 283 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 147 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 335 optimal weight: 30.0000 chunk 271 optimal weight: 30.0000 chunk 156 optimal weight: 0.2980 chunk 198 optimal weight: 0.0270 chunk 258 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.152521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.128795 restraints weight = 85632.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.126998 restraints weight = 122451.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.125406 restraints weight = 92806.540| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29280 Z= 0.112 Angle : 0.607 12.864 40037 Z= 0.307 Chirality : 0.044 0.223 4674 Planarity : 0.005 0.097 5152 Dihedral : 4.516 40.598 4240 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.79 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3992 helix: 1.27 (0.15), residues: 1255 sheet: -1.27 (0.19), residues: 793 loop : -2.36 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 315 HIS 0.006 0.001 HIS B 61 PHE 0.026 0.001 PHE B 241 TYR 0.035 0.001 TYR C 795 ARG 0.006 0.000 ARG D 742 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 1103) hydrogen bonds : angle 4.29572 ( 3237) SS BOND : bond 0.00300 ( 22) SS BOND : angle 1.30634 ( 44) covalent geometry : bond 0.00261 (29258) covalent geometry : angle 0.60545 (39993) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TRP cc_start: 0.7875 (p-90) cc_final: 0.7599 (p-90) REVERT: A 354 MET cc_start: 0.8412 (tpp) cc_final: 0.7314 (tmm) REVERT: B 157 MET cc_start: 0.8130 (ptp) cc_final: 0.7880 (ptp) REVERT: B 418 ILE cc_start: 0.7115 (pt) cc_final: 0.6886 (pt) REVERT: B 565 MET cc_start: 0.6968 (mmm) cc_final: 0.6728 (mmm) REVERT: C 41 MET cc_start: 0.8290 (pmm) cc_final: 0.8063 (pmm) REVERT: C 119 LEU cc_start: 0.7846 (mm) cc_final: 0.7524 (mt) REVERT: C 184 LEU cc_start: 0.8556 (pp) cc_final: 0.8181 (mt) REVERT: C 322 LYS cc_start: 0.5195 (mmtt) cc_final: 0.4899 (mptt) REVERT: C 819 ILE cc_start: 0.8106 (tp) cc_final: 0.7762 (tp) REVERT: D 134 MET cc_start: 0.5256 (tmm) cc_final: 0.5014 (tmm) REVERT: K 89 GLN cc_start: -0.0313 (pm20) cc_final: -0.0646 (pp30) REVERT: K 102 GLN cc_start: 0.2167 (pm20) cc_final: 0.1794 (tp40) REVERT: K 125 GLU cc_start: 0.1275 (mm-30) cc_final: 0.0035 (pt0) REVERT: K 185 LYS cc_start: -0.1131 (tptm) cc_final: -0.1380 (tptp) REVERT: K 197 GLU cc_start: 0.5693 (tm-30) cc_final: 0.5350 (tm-30) REVERT: L 165 VAL cc_start: 0.4562 (t) cc_final: 0.4311 (t) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.3532 time to fit residues: 202.1748 Evaluate side-chains 283 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 301 optimal weight: 10.0000 chunk 286 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 291 optimal weight: 7.9990 chunk 319 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 320 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 283 optimal weight: 10.0000 overall best weight: 3.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS D 145 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.148819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.123694 restraints weight = 85124.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.122147 restraints weight = 139140.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.120733 restraints weight = 102824.829| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 29280 Z= 0.229 Angle : 0.714 12.410 40037 Z= 0.369 Chirality : 0.047 0.261 4674 Planarity : 0.005 0.098 5152 Dihedral : 4.942 30.206 4240 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.12 % Favored : 88.63 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3992 helix: 0.95 (0.15), residues: 1247 sheet: -1.33 (0.20), residues: 759 loop : -2.43 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 56 HIS 0.022 0.001 HIS A 780 PHE 0.021 0.002 PHE C 533 TYR 0.034 0.002 TYR C 795 ARG 0.005 0.001 ARG D 742 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 1103) hydrogen bonds : angle 4.71045 ( 3237) SS BOND : bond 0.00407 ( 22) SS BOND : angle 1.56175 ( 44) covalent geometry : bond 0.00541 (29258) covalent geometry : angle 0.71224 (39993) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TRP cc_start: 0.8026 (p-90) cc_final: 0.7731 (p-90) REVERT: A 424 PHE cc_start: 0.7841 (m-80) cc_final: 0.7313 (m-80) REVERT: B 157 MET cc_start: 0.8229 (ptp) cc_final: 0.7983 (ptp) REVERT: C 41 MET cc_start: 0.8307 (pmm) cc_final: 0.8084 (pmm) REVERT: C 322 LYS cc_start: 0.5547 (mmtt) cc_final: 0.5289 (mptt) REVERT: C 819 ILE cc_start: 0.8420 (tp) cc_final: 0.8059 (tp) REVERT: D 134 MET cc_start: 0.5225 (tmm) cc_final: 0.5023 (tmm) REVERT: D 142 MET cc_start: 0.1204 (ttt) cc_final: 0.0980 (ttt) REVERT: K 89 GLN cc_start: -0.0147 (pm20) cc_final: -0.0556 (pp30) REVERT: K 125 GLU cc_start: 0.0964 (mm-30) cc_final: -0.0111 (pt0) REVERT: K 197 GLU cc_start: 0.5715 (tm-30) cc_final: 0.5322 (tm-30) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.3541 time to fit residues: 187.4743 Evaluate side-chains 267 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 325 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 360 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 270 optimal weight: 0.2980 chunk 234 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 359 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 449 HIS B 192 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN D 336 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.149387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.125286 restraints weight = 84476.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.121873 restraints weight = 123330.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.119208 restraints weight = 106269.715| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 29280 Z= 0.192 Angle : 0.680 12.354 40037 Z= 0.348 Chirality : 0.046 0.232 4674 Planarity : 0.005 0.097 5152 Dihedral : 4.907 35.222 4240 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.27 % Favored : 89.48 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3992 helix: 1.00 (0.15), residues: 1245 sheet: -1.32 (0.20), residues: 775 loop : -2.45 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 56 HIS 0.014 0.001 HIS A 780 PHE 0.023 0.002 PHE H 102 TYR 0.043 0.002 TYR A 109 ARG 0.005 0.001 ARG D 742 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 1103) hydrogen bonds : angle 4.60167 ( 3237) SS BOND : bond 0.00380 ( 22) SS BOND : angle 1.41075 ( 44) covalent geometry : bond 0.00458 (29258) covalent geometry : angle 0.67879 (39993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8599.02 seconds wall clock time: 151 minutes 27.37 seconds (9087.37 seconds total)