Starting phenix.real_space_refine on Fri Feb 6 08:21:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rcv_53923/02_2026/9rcv_53923.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rcv_53923/02_2026/9rcv_53923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rcv_53923/02_2026/9rcv_53923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rcv_53923/02_2026/9rcv_53923.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rcv_53923/02_2026/9rcv_53923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rcv_53923/02_2026/9rcv_53923.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 91 5.16 5 C 14980 2.51 5 N 4105 2.21 5 O 4346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23529 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5509 Classifications: {'peptide': 719} Link IDs: {'PTRANS': 31, 'TRANS': 687} Chain breaks: 1 Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2943 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 338} Chain breaks: 5 Chain: "C" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2246 Classifications: {'peptide': 274} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 258} Chain: "D" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "E" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5180 Classifications: {'peptide': 667} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 637} Chain breaks: 1 Chain: "F" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3040 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 353} Chain breaks: 2 Chain: "G" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2246 Classifications: {'peptide': 274} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 258} Chain: "H" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "I" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 559 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.38, per 1000 atoms: 0.23 Number of scatterers: 23529 At special positions: 0 Unit cell: (107.9, 153.55, 235.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 91 16.00 P 5 15.00 Mg 2 11.99 O 4346 8.00 N 4105 7.00 C 14980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 203 " - pdb=" SG CYS C 259 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 71 " distance=2.03 Simple disulfide: pdb=" SG CYS F 295 " - pdb=" SG CYS F 362 " distance=2.03 Simple disulfide: pdb=" SG CYS G 101 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 203 " - pdb=" SG CYS G 259 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 80 " distance=2.03 Simple disulfide: pdb=" SG CYS I 82 " - pdb=" SG CYS I 108 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 110 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG C 401 " - " ASN C 86 " " NAG G 401 " - " ASN G 86 " " NAG J 1 " - " ASN B 233 " " NAG K 1 " - " ASN F 233 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 918.5 milliseconds 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5520 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 29 sheets defined 44.0% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 17 through 48 removed outlier: 3.797A pdb=" N LEU A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG A 37 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 52 through 82 removed outlier: 4.116A pdb=" N SER A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 95 through 118 removed outlier: 5.078A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.591A pdb=" N SER A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 136 through 160 Proline residue: A 149 - end of helix removed outlier: 3.699A pdb=" N LEU A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 183 through 209 removed outlier: 3.837A pdb=" N LEU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 223 through 270 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 290 through 324 Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.613A pdb=" N THR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 373 removed outlier: 4.900A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix removed outlier: 4.985A pdb=" N LYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 436 removed outlier: 3.765A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 484 removed outlier: 3.922A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Proline residue: A 466 - end of helix removed outlier: 4.929A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 628 removed outlier: 3.681A pdb=" N GLY A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 674 through 687 Processing helix chain 'A' and resid 688 through 694 removed outlier: 3.766A pdb=" N TYR A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 709 removed outlier: 4.001A pdb=" N GLN A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 84 through 90 removed outlier: 4.426A pdb=" N GLY B 88 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 89 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 90 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 407 Processing helix chain 'C' and resid 56 through 85 removed outlier: 3.596A pdb=" N TRP C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 151 through 162 removed outlier: 3.986A pdb=" N GLN C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'E' and resid 8 through 25 Processing helix chain 'E' and resid 25 through 31 removed outlier: 3.781A pdb=" N THR E 29 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 30 " --> pdb=" O PRO E 26 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 31' Processing helix chain 'E' and resid 34 through 57 removed outlier: 3.642A pdb=" N ARG E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 65 through 84 removed outlier: 5.099A pdb=" N THR E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Proline residue: E 74 - end of helix Processing helix chain 'E' and resid 98 through 120 removed outlier: 3.825A pdb=" N LEU E 102 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 Processing helix chain 'E' and resid 148 through 182 removed outlier: 3.551A pdb=" N LEU E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Proline residue: E 170 - end of helix Processing helix chain 'E' and resid 185 through 234 Processing helix chain 'E' and resid 237 through 244 removed outlier: 3.757A pdb=" N PHE E 241 " --> pdb=" O ASP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 261 removed outlier: 4.837A pdb=" N THR E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 289 removed outlier: 3.949A pdb=" N ASN E 269 " --> pdb=" O PRO E 265 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 298 through 338 removed outlier: 4.672A pdb=" N PHE E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 344 Processing helix chain 'E' and resid 347 through 402 Processing helix chain 'E' and resid 405 through 440 removed outlier: 3.864A pdb=" N ALA E 440 " --> pdb=" O ASN E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 449 removed outlier: 3.802A pdb=" N PHE E 444 " --> pdb=" O ALA E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 517 Processing helix chain 'E' and resid 535 through 537 No H-bonds generated for 'chain 'E' and resid 535 through 537' Processing helix chain 'E' and resid 538 through 545 Processing helix chain 'E' and resid 559 through 565 Processing helix chain 'E' and resid 572 through 583 Processing helix chain 'E' and resid 585 through 590 removed outlier: 3.509A pdb=" N GLN E 590 " --> pdb=" O ASP E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 598 Processing helix chain 'E' and resid 601 through 605 Processing helix chain 'E' and resid 608 through 622 Processing helix chain 'E' and resid 638 through 645 Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 53 through 61 removed outlier: 3.596A pdb=" N PHE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 88 removed outlier: 4.488A pdb=" N GLY F 88 " --> pdb=" O TRP F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 100 removed outlier: 3.703A pdb=" N LEU F 99 " --> pdb=" O PRO F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 removed outlier: 4.152A pdb=" N LEU F 131 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 246 Processing helix chain 'F' and resid 352 through 356 Processing helix chain 'F' and resid 389 through 410 Processing helix chain 'G' and resid 57 through 86 removed outlier: 3.680A pdb=" N ASN G 63 " --> pdb=" O TYR G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.503A pdb=" N THR G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 162 removed outlier: 4.002A pdb=" N GLN G 155 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 175 Processing helix chain 'G' and resid 175 through 180 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.522A pdb=" N VAL I 85 " --> pdb=" O CYS I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 100 Processing helix chain 'I' and resid 110 through 115 Processing helix chain 'I' and resid 116 through 125 Processing helix chain 'I' and resid 125 through 150 removed outlier: 3.558A pdb=" N LEU I 140 " --> pdb=" O GLY I 136 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 528 removed outlier: 6.716A pdb=" N GLN A 522 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A 509 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU A 524 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 584 removed outlier: 6.630A pdb=" N ALA A 582 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASP A 667 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 584 " --> pdb=" O ASP A 667 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 158 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 230 through 238 current: chain 'B' and resid 103 through 109 removed outlier: 3.895A pdb=" N TRP B 103 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N CYS B 71 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG B 75 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N LEU B 46 " --> pdb=" O PRO B 22 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 24 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL B 48 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B 26 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR B 45 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA B 135 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER B 47 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL B 137 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N HIS B 49 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N LEU B 139 " --> pdb=" O HIS B 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.947A pdb=" N ARG B 188 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU B 196 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N HIS B 190 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 273 through 277 removed outlier: 5.892A pdb=" N VAL B 340 " --> pdb=" O HIS B 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 5.892A pdb=" N VAL B 340 " --> pdb=" O HIS B 299 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 321 through 322 removed outlier: 3.660A pdb=" N GLN B 321 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 46 through 47 removed outlier: 5.420A pdb=" N GLN C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL C 28 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 34 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG C 111 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP C 114 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ALA C 125 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR C 116 " --> pdb=" O TYR C 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 195 removed outlier: 6.363A pdb=" N GLU C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE C 241 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 186 through 195 removed outlier: 6.363A pdb=" N GLU C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE C 241 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 222 through 223 Processing sheet with id=AB4, first strand: chain 'D' and resid 6 through 11 removed outlier: 5.959A pdb=" N PHE D 62 " --> pdb=" O GLY D 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 6 through 11 removed outlier: 5.959A pdb=" N PHE D 62 " --> pdb=" O GLY D 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AB7, first strand: chain 'E' and resid 486 through 493 removed outlier: 6.645A pdb=" N LYS E 487 " --> pdb=" O SER E 474 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER E 474 " --> pdb=" O LYS E 487 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU E 489 " --> pdb=" O ASP E 472 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL E 473 " --> pdb=" O GLY E 524 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY E 524 " --> pdb=" O VAL E 473 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 546 through 549 removed outlier: 6.664A pdb=" N LEU E 628 " --> pdb=" O LEU E 657 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE E 659 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU E 630 " --> pdb=" O ILE E 659 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR E 499 " --> pdb=" O VAL E 658 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA E 660 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU E 501 " --> pdb=" O ALA E 660 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL E 498 " --> pdb=" O GLN E 671 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU E 673 " --> pdb=" O VAL E 498 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA E 500 " --> pdb=" O LEU E 673 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU E 675 " --> pdb=" O ALA E 500 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL E 502 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL E 674 " --> pdb=" O GLN E 681 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 216 through 221 removed outlier: 4.018A pdb=" N THR F 235 " --> pdb=" O PHE F 218 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU F 118 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR F 140 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER F 116 " --> pdb=" O THR F 140 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU F 142 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER F 114 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP F 103 " --> pdb=" O PHE F 76 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N CYS F 71 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG F 75 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR F 45 " --> pdb=" O THR F 133 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA F 135 " --> pdb=" O TYR F 45 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER F 47 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL F 137 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N HIS F 49 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N LEU F 139 " --> pdb=" O HIS F 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 149 through 151 removed outlier: 6.890A pdb=" N ARG F 188 " --> pdb=" O LEU F 196 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU F 196 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 273 through 276 removed outlier: 5.985A pdb=" N VAL F 340 " --> pdb=" O HIS F 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 273 through 276 removed outlier: 5.985A pdb=" N VAL F 340 " --> pdb=" O HIS F 299 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 321 through 322 Processing sheet with id=AC5, first strand: chain 'G' and resid 46 through 47 removed outlier: 6.631A pdb=" N GLY G 26 " --> pdb=" O PHE G 33 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG G 35 " --> pdb=" O SER G 24 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER G 24 " --> pdb=" O ARG G 35 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP G 37 " --> pdb=" O PHE G 22 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE G 22 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP G 114 " --> pdb=" O ALA G 125 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA G 125 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR G 116 " --> pdb=" O TYR G 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 186 through 195 removed outlier: 3.670A pdb=" N HIS G 188 " --> pdb=" O TRP G 204 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N PHE G 241 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 186 through 195 removed outlier: 3.670A pdb=" N HIS G 188 " --> pdb=" O TRP G 204 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N PHE G 241 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 222 through 223 Processing sheet with id=AC9, first strand: chain 'H' and resid 6 through 11 removed outlier: 5.781A pdb=" N PHE H 62 " --> pdb=" O GLY H 29 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 6 through 11 removed outlier: 5.781A pdb=" N PHE H 62 " --> pdb=" O GLY H 29 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 44 through 45 1436 hydrogen bonds defined for protein. 3999 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: 4.43 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7739 1.34 - 1.46: 5068 1.46 - 1.58: 11170 1.58 - 1.70: 8 1.70 - 1.82: 136 Bond restraints: 24121 Sorted by residual: bond pdb=" C4 ADP E 701 " pdb=" C5 ADP E 701 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C5 ADP E 701 " pdb=" C6 ADP E 701 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" N LEU A 130 " pdb=" CA LEU A 130 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.16e-02 7.43e+03 6.53e+00 bond pdb=" N GLY A 17 " pdb=" CA GLY A 17 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.27e+00 bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.01e+00 ... (remaining 24116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 32555 2.17 - 4.35: 285 4.35 - 6.52: 11 6.52 - 8.70: 5 8.70 - 10.87: 4 Bond angle restraints: 32860 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 132.58 7.29 1.00e+00 1.00e+00 5.31e+01 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 132.53 4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" PA ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PB ADP E 701 " ideal model delta sigma weight residual 120.50 131.37 -10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" CA LEU A 130 " pdb=" C LEU A 130 " pdb=" O LEU A 130 " ideal model delta sigma weight residual 121.07 117.46 3.61 1.10e+00 8.26e-01 1.08e+01 angle pdb=" N1 ADP E 701 " pdb=" C2 ADP E 701 " pdb=" N3 ADP E 701 " ideal model delta sigma weight residual 120.00 129.19 -9.19 3.00e+00 1.11e-01 9.39e+00 ... (remaining 32855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.58: 13818 18.58 - 37.16: 532 37.16 - 55.74: 99 55.74 - 74.32: 18 74.32 - 92.90: 17 Dihedral angle restraints: 14484 sinusoidal: 5893 harmonic: 8591 Sorted by residual: dihedral pdb=" O2A ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PA ADP E 701 " pdb=" PB ADP E 701 " ideal model delta sinusoidal sigma weight residual -60.00 -152.90 92.90 1 2.00e+01 2.50e-03 2.52e+01 dihedral pdb=" CA HIS B 254 " pdb=" C HIS B 254 " pdb=" N LEU B 255 " pdb=" CA LEU B 255 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA TYR C 27 " pdb=" C TYR C 27 " pdb=" N VAL C 28 " pdb=" CA VAL C 28 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 14481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2634 0.035 - 0.071: 753 0.071 - 0.106: 184 0.106 - 0.141: 77 0.141 - 0.177: 3 Chirality restraints: 3651 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.12e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.14e+01 chirality pdb=" C5 NAG J 1 " pdb=" C4 NAG J 1 " pdb=" C6 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.59 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 3648 not shown) Planarity restraints: 4243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " -0.121 2.00e-02 2.50e+03 9.92e-02 1.23e+02 pdb=" C7 NAG J 1 " 0.031 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.090 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " 0.159 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.097 2.00e-02 2.50e+03 8.02e-02 8.04e+01 pdb=" C7 NAG K 1 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.074 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.127 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 233 " 0.025 2.00e-02 2.50e+03 2.63e-02 8.66e+00 pdb=" CG ASN B 233 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 233 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 233 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.031 2.00e-02 2.50e+03 ... (remaining 4240 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 10 2.50 - 3.10: 16695 3.10 - 3.70: 34861 3.70 - 4.30: 51988 4.30 - 4.90: 88238 Nonbonded interactions: 191792 Sorted by model distance: nonbonded pdb=" OG SER E 510 " pdb="MG MG E 702 " model vdw 1.902 2.170 nonbonded pdb="MG MG E 702 " pdb=" O HOH E 802 " model vdw 1.908 2.170 nonbonded pdb="MG MG E 702 " pdb=" O HOH E 801 " model vdw 1.910 2.170 nonbonded pdb=" OG SER A 545 " pdb="MG MG A 802 " model vdw 1.936 2.170 nonbonded pdb="MG MG A 802 " pdb=" O HOH A 901 " model vdw 2.112 2.170 ... (remaining 191787 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 'B' and (resid 1 through 124 or resid 128 through 407)) selection = (chain 'F' and (resid 1 through 124 or resid 128 through 169 or resid 176 throug \ h 279 or resid 283 through 351 or resid 354 through 407)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' } 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 individual isotropic 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: 11.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.630 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 24139 Z= 0.146 Angle : 0.520 10.871 32902 Z= 0.263 Chirality : 0.038 0.177 3651 Planarity : 0.004 0.099 4239 Dihedral : 10.990 92.905 8928 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.64 % Allowed : 2.93 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.16), residues: 2957 helix: 2.36 (0.15), residues: 1210 sheet: 0.90 (0.20), residues: 681 loop : 0.11 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 378 TYR 0.010 0.001 TYR H 63 PHE 0.014 0.001 PHE E 412 TRP 0.008 0.001 TRP C 244 HIS 0.004 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00291 (24121) covalent geometry : angle 0.51619 (32860) SS BOND : bond 0.00173 ( 12) SS BOND : angle 0.88573 ( 24) hydrogen bonds : bond 0.10801 ( 1343) hydrogen bonds : angle 5.58661 ( 3999) link_BETA1-4 : bond 0.05103 ( 2) link_BETA1-4 : angle 3.25473 ( 6) link_NAG-ASN : bond 0.04830 ( 4) link_NAG-ASN : angle 2.49636 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 353 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 136 HIS cc_start: 0.5594 (OUTLIER) cc_final: 0.4945 (m-70) REVERT: A 428 TYR cc_start: 0.7730 (t80) cc_final: 0.7514 (t80) REVERT: A 561 GLN cc_start: 0.8140 (pt0) cc_final: 0.7886 (mp10) REVERT: A 681 VAL cc_start: 0.8074 (p) cc_final: 0.7793 (m) REVERT: B 94 ASN cc_start: 0.8676 (p0) cc_final: 0.8449 (p0) REVERT: B 159 ASP cc_start: 0.8607 (t70) cc_final: 0.8290 (t70) REVERT: B 363 ARG cc_start: 0.7828 (tpp80) cc_final: 0.7608 (tpp80) REVERT: E 143 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7905 (tmtt) REVERT: E 401 ASP cc_start: 0.7925 (t70) cc_final: 0.7570 (t0) REVERT: E 575 LYS cc_start: 0.7299 (mmmt) cc_final: 0.7008 (mtmt) REVERT: E 602 GLU cc_start: 0.8162 (tt0) cc_final: 0.7937 (tt0) REVERT: E 615 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8531 (mp) REVERT: E 661 HIS cc_start: 0.7945 (t70) cc_final: 0.7660 (t70) REVERT: E 670 HIS cc_start: 0.7566 (t70) cc_final: 0.7345 (t-170) REVERT: F 94 ASN cc_start: 0.8338 (p0) cc_final: 0.7949 (p0) REVERT: G 163 GLU cc_start: 0.7714 (mp0) cc_final: 0.7116 (mp0) REVERT: G 178 LYS cc_start: 0.7829 (ptmt) cc_final: 0.7609 (pttm) REVERT: G 186 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8371 (mttp) REVERT: G 212 GLU cc_start: 0.7773 (mp0) cc_final: 0.7462 (pm20) REVERT: H 38 ASP cc_start: 0.8183 (m-30) cc_final: 0.7960 (m-30) REVERT: H 94 LYS cc_start: 0.7325 (mttp) cc_final: 0.7090 (ttmm) outliers start: 16 outliers final: 3 residues processed: 368 average time/residue: 0.8149 time to fit residues: 333.7566 Evaluate side-chains 273 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 268 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain F residue 308 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 708 GLN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 262 GLN E 242 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN E 670 HIS G 224 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.114673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087405 restraints weight = 46868.872| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.36 r_work: 0.3156 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24139 Z= 0.151 Angle : 0.560 9.758 32902 Z= 0.279 Chirality : 0.040 0.159 3651 Planarity : 0.004 0.041 4239 Dihedral : 5.456 69.093 3440 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.92 % Allowed : 8.46 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.16), residues: 2957 helix: 2.51 (0.15), residues: 1211 sheet: 1.07 (0.20), residues: 686 loop : 0.10 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 129 TYR 0.015 0.001 TYR H 63 PHE 0.022 0.002 PHE E 412 TRP 0.017 0.001 TRP G 244 HIS 0.006 0.001 HIS E 670 Details of bonding type rmsd covalent geometry : bond 0.00356 (24121) covalent geometry : angle 0.55720 (32860) SS BOND : bond 0.00279 ( 12) SS BOND : angle 1.09577 ( 24) hydrogen bonds : bond 0.04887 ( 1343) hydrogen bonds : angle 4.62968 ( 3999) link_BETA1-4 : bond 0.00282 ( 2) link_BETA1-4 : angle 1.31767 ( 6) link_NAG-ASN : bond 0.00215 ( 4) link_NAG-ASN : angle 2.47617 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 131 LEU cc_start: 0.3799 (OUTLIER) cc_final: 0.3333 (pt) REVERT: A 136 HIS cc_start: 0.4565 (OUTLIER) cc_final: 0.4318 (m-70) REVERT: A 428 TYR cc_start: 0.7811 (t80) cc_final: 0.7578 (t80) REVERT: A 561 GLN cc_start: 0.8270 (pt0) cc_final: 0.7933 (mp10) REVERT: A 678 GLN cc_start: 0.7279 (tt0) cc_final: 0.6749 (tm-30) REVERT: A 681 VAL cc_start: 0.8080 (p) cc_final: 0.7762 (m) REVERT: B 94 ASN cc_start: 0.8613 (p0) cc_final: 0.8384 (p0) REVERT: B 327 ARG cc_start: 0.7652 (ptp90) cc_final: 0.7408 (ptp90) REVERT: B 363 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7510 (tpp80) REVERT: C 70 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7187 (mt0) REVERT: C 170 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7703 (ttp-110) REVERT: E 143 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7790 (tmtt) REVERT: E 205 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8269 (mp) REVERT: E 401 ASP cc_start: 0.7996 (t70) cc_final: 0.7727 (t0) REVERT: E 575 LYS cc_start: 0.7333 (mmmt) cc_final: 0.7020 (mtmt) REVERT: E 602 GLU cc_start: 0.8146 (tt0) cc_final: 0.7944 (tt0) REVERT: E 672 ILE cc_start: 0.8806 (mm) cc_final: 0.8562 (mm) REVERT: F 94 ASN cc_start: 0.8238 (p0) cc_final: 0.7926 (p0) REVERT: F 165 MET cc_start: 0.9090 (tpt) cc_final: 0.8729 (tpt) REVERT: F 212 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8077 (mt0) REVERT: G 138 THR cc_start: 0.8727 (t) cc_final: 0.8399 (m) REVERT: G 163 GLU cc_start: 0.7792 (mp0) cc_final: 0.7183 (mp0) REVERT: G 178 LYS cc_start: 0.7872 (ptmt) cc_final: 0.7487 (pmtt) outliers start: 48 outliers final: 20 residues processed: 300 average time/residue: 0.7905 time to fit residues: 263.3743 Evaluate side-chains 290 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 34 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 192 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 291 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN C 72 GLN C 262 GLN E 242 GLN E 505 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089481 restraints weight = 46730.607| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.34 r_work: 0.3149 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24139 Z= 0.156 Angle : 0.547 8.101 32902 Z= 0.273 Chirality : 0.040 0.158 3651 Planarity : 0.004 0.045 4239 Dihedral : 5.285 64.184 3436 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.45 % Allowed : 9.34 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.16), residues: 2957 helix: 2.50 (0.15), residues: 1211 sheet: 1.13 (0.20), residues: 686 loop : 0.04 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 28 TYR 0.013 0.001 TYR H 63 PHE 0.023 0.002 PHE A 624 TRP 0.016 0.001 TRP G 244 HIS 0.006 0.001 HIS G 260 Details of bonding type rmsd covalent geometry : bond 0.00369 (24121) covalent geometry : angle 0.54443 (32860) SS BOND : bond 0.00349 ( 12) SS BOND : angle 1.07411 ( 24) hydrogen bonds : bond 0.04834 ( 1343) hydrogen bonds : angle 4.50563 ( 3999) link_BETA1-4 : bond 0.00224 ( 2) link_BETA1-4 : angle 1.31485 ( 6) link_NAG-ASN : bond 0.00219 ( 4) link_NAG-ASN : angle 2.46007 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 131 LEU cc_start: 0.3411 (OUTLIER) cc_final: 0.2982 (pt) REVERT: A 428 TYR cc_start: 0.7802 (t80) cc_final: 0.7564 (t80) REVERT: A 561 GLN cc_start: 0.8217 (pt0) cc_final: 0.7931 (mp10) REVERT: A 678 GLN cc_start: 0.7235 (tt0) cc_final: 0.6681 (tm-30) REVERT: A 681 VAL cc_start: 0.8055 (p) cc_final: 0.7723 (m) REVERT: B 273 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7416 (mtpt) REVERT: B 363 ARG cc_start: 0.7772 (tpp80) cc_final: 0.7443 (ttm-80) REVERT: C 70 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7165 (mt0) REVERT: C 170 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7481 (ttp-170) REVERT: C 253 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7245 (tt0) REVERT: E 143 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7745 (tmtt) REVERT: E 205 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8257 (mp) REVERT: E 401 ASP cc_start: 0.7999 (t70) cc_final: 0.7728 (t0) REVERT: E 575 LYS cc_start: 0.7304 (mmmt) cc_final: 0.7003 (mtmt) REVERT: E 615 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8608 (mp) REVERT: E 624 ASP cc_start: 0.8152 (t0) cc_final: 0.7863 (t0) REVERT: E 626 ARG cc_start: 0.8730 (tpp-160) cc_final: 0.8506 (tpp-160) REVERT: E 672 ILE cc_start: 0.8819 (mm) cc_final: 0.8565 (mm) REVERT: F 94 ASN cc_start: 0.8232 (p0) cc_final: 0.7900 (p0) REVERT: F 363 ARG cc_start: 0.7339 (ttt-90) cc_final: 0.7002 (mmm-85) REVERT: G 163 GLU cc_start: 0.7785 (mp0) cc_final: 0.7161 (mp0) REVERT: G 178 LYS cc_start: 0.7827 (ptmt) cc_final: 0.7448 (pmtt) REVERT: H 38 ASP cc_start: 0.8288 (m-30) cc_final: 0.8048 (m-30) outliers start: 61 outliers final: 32 residues processed: 305 average time/residue: 0.8406 time to fit residues: 286.5775 Evaluate side-chains 295 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 258 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 51 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 273 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 252 optimal weight: 0.4980 chunk 227 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN C 72 GLN E 242 GLN E 670 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.107692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.080888 restraints weight = 47022.314| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.21 r_work: 0.3175 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24139 Z= 0.136 Angle : 0.529 8.248 32902 Z= 0.263 Chirality : 0.039 0.154 3651 Planarity : 0.004 0.047 4239 Dihedral : 5.130 62.069 3433 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.53 % Allowed : 10.02 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.16), residues: 2957 helix: 2.54 (0.15), residues: 1222 sheet: 1.20 (0.20), residues: 686 loop : 0.05 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 327 TYR 0.013 0.001 TYR G 9 PHE 0.024 0.002 PHE A 624 TRP 0.015 0.001 TRP G 244 HIS 0.005 0.001 HIS G 260 Details of bonding type rmsd covalent geometry : bond 0.00315 (24121) covalent geometry : angle 0.52606 (32860) SS BOND : bond 0.00259 ( 12) SS BOND : angle 0.96463 ( 24) hydrogen bonds : bond 0.04596 ( 1343) hydrogen bonds : angle 4.39488 ( 3999) link_BETA1-4 : bond 0.00283 ( 2) link_BETA1-4 : angle 1.24483 ( 6) link_NAG-ASN : bond 0.00204 ( 4) link_NAG-ASN : angle 2.39502 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 264 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 131 LEU cc_start: 0.3358 (OUTLIER) cc_final: 0.2944 (pt) REVERT: A 343 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7719 (tptt) REVERT: A 428 TYR cc_start: 0.7813 (t80) cc_final: 0.7584 (t80) REVERT: A 561 GLN cc_start: 0.8227 (pt0) cc_final: 0.8008 (mp10) REVERT: A 681 VAL cc_start: 0.8135 (p) cc_final: 0.7796 (m) REVERT: B 273 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7362 (mtpt) REVERT: B 363 ARG cc_start: 0.7802 (tpp80) cc_final: 0.7541 (ttm-80) REVERT: C 170 ARG cc_start: 0.7965 (ttm170) cc_final: 0.7524 (ttp-110) REVERT: C 253 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7259 (tt0) REVERT: C 262 GLN cc_start: 0.8182 (mp10) cc_final: 0.7914 (mp10) REVERT: E 143 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7729 (tmtt) REVERT: E 401 ASP cc_start: 0.8000 (t70) cc_final: 0.7759 (t0) REVERT: E 574 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7407 (p0) REVERT: E 575 LYS cc_start: 0.7335 (mmmt) cc_final: 0.7048 (mtmt) REVERT: E 615 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8645 (mp) REVERT: E 624 ASP cc_start: 0.8165 (t0) cc_final: 0.7910 (t0) REVERT: E 626 ARG cc_start: 0.8757 (tpp-160) cc_final: 0.8539 (tpp-160) REVERT: F 94 ASN cc_start: 0.8215 (p0) cc_final: 0.7912 (p0) REVERT: G 138 THR cc_start: 0.8787 (t) cc_final: 0.8462 (m) REVERT: G 163 GLU cc_start: 0.7837 (mp0) cc_final: 0.7267 (mp0) REVERT: G 178 LYS cc_start: 0.7878 (ptmt) cc_final: 0.7620 (pttm) REVERT: G 216 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7552 (p) outliers start: 63 outliers final: 32 residues processed: 305 average time/residue: 0.8441 time to fit residues: 288.0223 Evaluate side-chains 293 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 19 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN C 72 GLN C 218 GLN E 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.106804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080113 restraints weight = 46977.976| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.17 r_work: 0.3145 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24139 Z= 0.175 Angle : 0.563 7.993 32902 Z= 0.279 Chirality : 0.041 0.159 3651 Planarity : 0.005 0.048 4239 Dihedral : 5.233 60.965 3433 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.29 % Allowed : 10.79 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.16), residues: 2957 helix: 2.43 (0.15), residues: 1223 sheet: 1.22 (0.20), residues: 685 loop : -0.00 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 44 TYR 0.014 0.002 TYR H 63 PHE 0.026 0.002 PHE A 624 TRP 0.016 0.001 TRP G 244 HIS 0.005 0.001 HIS G 260 Details of bonding type rmsd covalent geometry : bond 0.00421 (24121) covalent geometry : angle 0.56000 (32860) SS BOND : bond 0.00245 ( 12) SS BOND : angle 1.06982 ( 24) hydrogen bonds : bond 0.04901 ( 1343) hydrogen bonds : angle 4.45222 ( 3999) link_BETA1-4 : bond 0.00182 ( 2) link_BETA1-4 : angle 1.36596 ( 6) link_NAG-ASN : bond 0.00286 ( 4) link_NAG-ASN : angle 2.51110 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 259 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 131 LEU cc_start: 0.3234 (OUTLIER) cc_final: 0.2887 (pt) REVERT: A 133 TRP cc_start: 0.2705 (OUTLIER) cc_final: 0.1959 (m100) REVERT: A 231 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7322 (tmm) REVERT: A 428 TYR cc_start: 0.7824 (t80) cc_final: 0.7578 (t80) REVERT: A 561 GLN cc_start: 0.8221 (pt0) cc_final: 0.7982 (mp10) REVERT: A 678 GLN cc_start: 0.7318 (tt0) cc_final: 0.6746 (tm-30) REVERT: A 681 VAL cc_start: 0.8211 (p) cc_final: 0.7858 (m) REVERT: B 273 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7402 (mtpt) REVERT: B 363 ARG cc_start: 0.7797 (tpp80) cc_final: 0.7548 (ttm-80) REVERT: C 170 ARG cc_start: 0.7965 (ttm170) cc_final: 0.7548 (ttp-110) REVERT: C 253 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7233 (tt0) REVERT: C 262 GLN cc_start: 0.8160 (mp10) cc_final: 0.7918 (mp10) REVERT: E 143 LYS cc_start: 0.8246 (mtmt) cc_final: 0.7863 (tmtt) REVERT: E 401 ASP cc_start: 0.8023 (t70) cc_final: 0.7773 (t0) REVERT: E 574 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7391 (p0) REVERT: E 575 LYS cc_start: 0.7333 (mmmt) cc_final: 0.7039 (mtmt) REVERT: E 615 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8707 (mp) REVERT: E 624 ASP cc_start: 0.8177 (t0) cc_final: 0.7902 (t0) REVERT: E 626 ARG cc_start: 0.8789 (tpp-160) cc_final: 0.8574 (tpp-160) REVERT: F 93 GLN cc_start: 0.5325 (tp-100) cc_final: 0.5103 (tp40) REVERT: F 94 ASN cc_start: 0.8227 (p0) cc_final: 0.7901 (p0) REVERT: G 163 GLU cc_start: 0.7846 (mp0) cc_final: 0.7287 (mp0) REVERT: G 178 LYS cc_start: 0.7870 (ptmt) cc_final: 0.7606 (pttm) outliers start: 57 outliers final: 39 residues processed: 300 average time/residue: 0.8616 time to fit residues: 289.2025 Evaluate side-chains 297 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 116 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 159 optimal weight: 0.5980 chunk 6 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN C 72 GLN C 218 GLN E 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.112987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.087034 restraints weight = 46924.121| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.37 r_work: 0.3153 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24139 Z= 0.136 Angle : 0.530 7.830 32902 Z= 0.264 Chirality : 0.039 0.151 3651 Planarity : 0.004 0.048 4239 Dihedral : 5.154 60.300 3433 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.29 % Allowed : 11.31 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.16), residues: 2957 helix: 2.50 (0.15), residues: 1229 sheet: 1.34 (0.20), residues: 678 loop : -0.03 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 44 TYR 0.013 0.001 TYR H 63 PHE 0.025 0.002 PHE A 624 TRP 0.016 0.001 TRP C 244 HIS 0.007 0.001 HIS E 670 Details of bonding type rmsd covalent geometry : bond 0.00315 (24121) covalent geometry : angle 0.52796 (32860) SS BOND : bond 0.00218 ( 12) SS BOND : angle 0.90566 ( 24) hydrogen bonds : bond 0.04573 ( 1343) hydrogen bonds : angle 4.35851 ( 3999) link_BETA1-4 : bond 0.00314 ( 2) link_BETA1-4 : angle 1.22143 ( 6) link_NAG-ASN : bond 0.00199 ( 4) link_NAG-ASN : angle 2.41041 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.3219 (OUTLIER) cc_final: 0.2807 (pt) REVERT: A 133 TRP cc_start: 0.2507 (OUTLIER) cc_final: 0.1790 (m100) REVERT: A 343 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7736 (tptt) REVERT: A 428 TYR cc_start: 0.7771 (t80) cc_final: 0.7539 (t80) REVERT: A 561 GLN cc_start: 0.8177 (pt0) cc_final: 0.7947 (mp10) REVERT: A 678 GLN cc_start: 0.7291 (tt0) cc_final: 0.6678 (tm-30) REVERT: A 681 VAL cc_start: 0.8091 (p) cc_final: 0.7724 (m) REVERT: B 363 ARG cc_start: 0.7771 (tpp80) cc_final: 0.7544 (ttm-80) REVERT: C 170 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7509 (ttp-110) REVERT: C 253 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7277 (tt0) REVERT: C 262 GLN cc_start: 0.8163 (mp10) cc_final: 0.7895 (mp10) REVERT: E 143 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7703 (tmtt) REVERT: E 401 ASP cc_start: 0.8030 (t70) cc_final: 0.7776 (t0) REVERT: E 574 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7417 (p0) REVERT: E 575 LYS cc_start: 0.7311 (mmmt) cc_final: 0.7021 (mtmt) REVERT: E 615 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8660 (mp) REVERT: E 624 ASP cc_start: 0.8174 (t0) cc_final: 0.7890 (t0) REVERT: E 626 ARG cc_start: 0.8764 (tpp-160) cc_final: 0.8548 (tpp-160) REVERT: F 94 ASN cc_start: 0.8247 (p0) cc_final: 0.7937 (p0) REVERT: G 163 GLU cc_start: 0.7816 (mp0) cc_final: 0.7239 (mp0) REVERT: G 178 LYS cc_start: 0.7871 (ptmt) cc_final: 0.7594 (pttm) outliers start: 57 outliers final: 40 residues processed: 302 average time/residue: 0.8729 time to fit residues: 294.4628 Evaluate side-chains 304 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 282 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 281 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN B 94 ASN C 72 GLN C 218 GLN E 242 GLN G 260 HIS ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.113965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086831 restraints weight = 46392.556| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.32 r_work: 0.3117 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 24139 Z= 0.242 Angle : 0.620 7.939 32902 Z= 0.307 Chirality : 0.043 0.165 3651 Planarity : 0.005 0.059 4239 Dihedral : 5.384 63.895 3433 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.61 % Allowed : 11.31 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.16), residues: 2957 helix: 2.27 (0.15), residues: 1218 sheet: 1.25 (0.20), residues: 680 loop : -0.10 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 210 TYR 0.017 0.002 TYR A 601 PHE 0.027 0.003 PHE A 624 TRP 0.016 0.002 TRP G 244 HIS 0.006 0.001 HIS G 260 Details of bonding type rmsd covalent geometry : bond 0.00593 (24121) covalent geometry : angle 0.61706 (32860) SS BOND : bond 0.00300 ( 12) SS BOND : angle 1.34048 ( 24) hydrogen bonds : bond 0.05395 ( 1343) hydrogen bonds : angle 4.57109 ( 3999) link_BETA1-4 : bond 0.00064 ( 2) link_BETA1-4 : angle 1.50783 ( 6) link_NAG-ASN : bond 0.00406 ( 4) link_NAG-ASN : angle 2.69676 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 253 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.4154 (OUTLIER) cc_final: 0.3804 (mt) REVERT: A 131 LEU cc_start: 0.3329 (OUTLIER) cc_final: 0.2817 (pt) REVERT: A 133 TRP cc_start: 0.2706 (OUTLIER) cc_final: 0.2013 (m100) REVERT: A 231 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7433 (tmm) REVERT: A 428 TYR cc_start: 0.7869 (t80) cc_final: 0.7632 (t80) REVERT: A 561 GLN cc_start: 0.8219 (pt0) cc_final: 0.7958 (mp10) REVERT: A 681 VAL cc_start: 0.8212 (p) cc_final: 0.7866 (m) REVERT: B 363 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7587 (ttm-80) REVERT: C 170 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7375 (ttp-170) REVERT: C 253 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7228 (tt0) REVERT: C 262 GLN cc_start: 0.8189 (mp10) cc_final: 0.7972 (mp10) REVERT: E 143 LYS cc_start: 0.8277 (mtmt) cc_final: 0.7921 (tmtt) REVERT: E 401 ASP cc_start: 0.8048 (t70) cc_final: 0.7803 (t0) REVERT: E 574 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7432 (p0) REVERT: E 575 LYS cc_start: 0.7343 (mmmt) cc_final: 0.7027 (mtmt) REVERT: E 615 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8747 (mp) REVERT: E 624 ASP cc_start: 0.8215 (t0) cc_final: 0.7946 (t0) REVERT: E 626 ARG cc_start: 0.8829 (tpp-160) cc_final: 0.8609 (tpp-160) REVERT: F 94 ASN cc_start: 0.8248 (p0) cc_final: 0.7932 (p0) REVERT: G 163 GLU cc_start: 0.7839 (mp0) cc_final: 0.7338 (mp0) REVERT: G 178 LYS cc_start: 0.7910 (ptmt) cc_final: 0.7653 (pttm) outliers start: 65 outliers final: 39 residues processed: 300 average time/residue: 0.8613 time to fit residues: 289.0283 Evaluate side-chains 288 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 10 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 163 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 217 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 286 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN B 94 ASN C 72 GLN C 218 GLN H 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088772 restraints weight = 46492.657| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.47 r_work: 0.3143 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24139 Z= 0.138 Angle : 0.545 7.693 32902 Z= 0.271 Chirality : 0.039 0.151 3651 Planarity : 0.004 0.048 4239 Dihedral : 5.168 66.002 3433 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.25 % Allowed : 12.07 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.16), residues: 2957 helix: 2.44 (0.15), residues: 1223 sheet: 1.33 (0.20), residues: 677 loop : -0.03 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 210 TYR 0.014 0.001 TYR H 63 PHE 0.027 0.002 PHE A 624 TRP 0.018 0.001 TRP C 244 HIS 0.007 0.001 HIS E 670 Details of bonding type rmsd covalent geometry : bond 0.00319 (24121) covalent geometry : angle 0.54257 (32860) SS BOND : bond 0.00242 ( 12) SS BOND : angle 0.96575 ( 24) hydrogen bonds : bond 0.04679 ( 1343) hydrogen bonds : angle 4.39916 ( 3999) link_BETA1-4 : bond 0.00349 ( 2) link_BETA1-4 : angle 1.22875 ( 6) link_NAG-ASN : bond 0.00214 ( 4) link_NAG-ASN : angle 2.48958 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 249 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.4127 (OUTLIER) cc_final: 0.3782 (mt) REVERT: A 131 LEU cc_start: 0.3379 (OUTLIER) cc_final: 0.2849 (pt) REVERT: A 133 TRP cc_start: 0.2532 (OUTLIER) cc_final: 0.1858 (m100) REVERT: A 215 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7910 (pp) REVERT: A 428 TYR cc_start: 0.7783 (t80) cc_final: 0.7547 (t80) REVERT: A 561 GLN cc_start: 0.8159 (pt0) cc_final: 0.7933 (mp10) REVERT: A 681 VAL cc_start: 0.8149 (p) cc_final: 0.7824 (m) REVERT: B 363 ARG cc_start: 0.7802 (tpp80) cc_final: 0.7550 (ttm-80) REVERT: C 170 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7362 (ttp-170) REVERT: C 253 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7307 (tt0) REVERT: C 262 GLN cc_start: 0.8151 (mp10) cc_final: 0.7836 (mp10) REVERT: E 143 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7737 (tmtt) REVERT: E 401 ASP cc_start: 0.8015 (t70) cc_final: 0.7770 (t0) REVERT: E 574 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7407 (p0) REVERT: E 575 LYS cc_start: 0.7327 (mmmt) cc_final: 0.7030 (mtmt) REVERT: E 615 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8696 (mp) REVERT: E 624 ASP cc_start: 0.8199 (t0) cc_final: 0.7924 (t0) REVERT: E 626 ARG cc_start: 0.8783 (tpp-160) cc_final: 0.8565 (tpp-160) REVERT: F 94 ASN cc_start: 0.8244 (p0) cc_final: 0.7927 (p0) REVERT: G 163 GLU cc_start: 0.7830 (mp0) cc_final: 0.7256 (mp0) REVERT: G 178 LYS cc_start: 0.7889 (ptmt) cc_final: 0.7628 (pttm) outliers start: 56 outliers final: 40 residues processed: 290 average time/residue: 0.8164 time to fit residues: 264.1070 Evaluate side-chains 296 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 209 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 168 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 214 optimal weight: 0.1980 chunk 127 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 187 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN B 94 ASN C 218 GLN E 267 ASN H 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.115226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.088772 restraints weight = 46528.840| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.43 r_work: 0.3161 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24139 Z= 0.127 Angle : 0.529 7.586 32902 Z= 0.264 Chirality : 0.039 0.148 3651 Planarity : 0.004 0.048 4239 Dihedral : 5.026 67.903 3433 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.04 % Allowed : 12.39 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.16), residues: 2957 helix: 2.55 (0.15), residues: 1225 sheet: 1.37 (0.20), residues: 670 loop : -0.03 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 210 TYR 0.013 0.001 TYR D 63 PHE 0.030 0.002 PHE A 624 TRP 0.018 0.001 TRP G 244 HIS 0.008 0.001 HIS E 670 Details of bonding type rmsd covalent geometry : bond 0.00290 (24121) covalent geometry : angle 0.52644 (32860) SS BOND : bond 0.00229 ( 12) SS BOND : angle 0.89344 ( 24) hydrogen bonds : bond 0.04435 ( 1343) hydrogen bonds : angle 4.29713 ( 3999) link_BETA1-4 : bond 0.00293 ( 2) link_BETA1-4 : angle 1.19997 ( 6) link_NAG-ASN : bond 0.00206 ( 4) link_NAG-ASN : angle 2.39905 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.4096 (OUTLIER) cc_final: 0.3782 (mt) REVERT: A 131 LEU cc_start: 0.3460 (OUTLIER) cc_final: 0.2911 (pt) REVERT: A 133 TRP cc_start: 0.2432 (OUTLIER) cc_final: 0.1705 (m100) REVERT: A 215 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7858 (pp) REVERT: A 428 TYR cc_start: 0.7702 (t80) cc_final: 0.7469 (t80) REVERT: A 561 GLN cc_start: 0.8103 (pt0) cc_final: 0.7872 (mp10) REVERT: A 681 VAL cc_start: 0.8053 (p) cc_final: 0.7721 (m) REVERT: B 61 ARG cc_start: 0.7189 (mmp80) cc_final: 0.6912 (mmp80) REVERT: B 159 ASP cc_start: 0.8721 (t70) cc_final: 0.8480 (t70) REVERT: B 327 ARG cc_start: 0.7676 (ptp90) cc_final: 0.7298 (mtt180) REVERT: B 363 ARG cc_start: 0.7759 (tpp80) cc_final: 0.7526 (ttm-80) REVERT: C 170 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7285 (ttp-170) REVERT: C 253 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7282 (tt0) REVERT: C 262 GLN cc_start: 0.8108 (mp10) cc_final: 0.7878 (mp10) REVERT: E 143 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7678 (tmtt) REVERT: E 401 ASP cc_start: 0.8018 (t70) cc_final: 0.7762 (t0) REVERT: E 575 LYS cc_start: 0.7245 (mmmt) cc_final: 0.6976 (mtmt) REVERT: E 615 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8619 (mp) REVERT: E 624 ASP cc_start: 0.8161 (t0) cc_final: 0.7868 (t0) REVERT: E 626 ARG cc_start: 0.8745 (tpp-160) cc_final: 0.8532 (tpp-160) REVERT: F 94 ASN cc_start: 0.8266 (p0) cc_final: 0.7968 (p0) REVERT: G 163 GLU cc_start: 0.7773 (mp0) cc_final: 0.7202 (mp0) REVERT: G 178 LYS cc_start: 0.7832 (ptmt) cc_final: 0.7561 (pttm) REVERT: G 216 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7492 (p) outliers start: 51 outliers final: 37 residues processed: 299 average time/residue: 0.7678 time to fit residues: 257.8036 Evaluate side-chains 297 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 69 optimal weight: 7.9990 chunk 223 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 275 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN C 72 GLN C 218 GLN H 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.115940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.089738 restraints weight = 46326.664| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.43 r_work: 0.3155 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24139 Z= 0.139 Angle : 0.546 7.541 32902 Z= 0.272 Chirality : 0.039 0.172 3651 Planarity : 0.004 0.049 4239 Dihedral : 5.022 69.307 3433 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.00 % Allowed : 12.59 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.16), residues: 2957 helix: 2.55 (0.15), residues: 1223 sheet: 1.38 (0.20), residues: 670 loop : -0.06 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 210 TYR 0.018 0.001 TYR G 67 PHE 0.030 0.002 PHE A 624 TRP 0.016 0.001 TRP G 244 HIS 0.008 0.001 HIS E 670 Details of bonding type rmsd covalent geometry : bond 0.00326 (24121) covalent geometry : angle 0.54385 (32860) SS BOND : bond 0.00234 ( 12) SS BOND : angle 0.94350 ( 24) hydrogen bonds : bond 0.04511 ( 1343) hydrogen bonds : angle 4.30236 ( 3999) link_BETA1-4 : bond 0.00236 ( 2) link_BETA1-4 : angle 1.23591 ( 6) link_NAG-ASN : bond 0.00230 ( 4) link_NAG-ASN : angle 2.45336 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5914 Ramachandran restraints generated. 2957 Oldfield, 0 Emsley, 2957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.4087 (OUTLIER) cc_final: 0.3783 (mt) REVERT: A 131 LEU cc_start: 0.3419 (OUTLIER) cc_final: 0.2839 (pt) REVERT: A 133 TRP cc_start: 0.2388 (OUTLIER) cc_final: 0.1662 (m100) REVERT: A 215 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7868 (pp) REVERT: A 428 TYR cc_start: 0.7731 (t80) cc_final: 0.7492 (t80) REVERT: A 561 GLN cc_start: 0.8101 (pt0) cc_final: 0.7886 (mp10) REVERT: A 681 VAL cc_start: 0.8077 (p) cc_final: 0.7745 (m) REVERT: B 61 ARG cc_start: 0.7230 (mmp80) cc_final: 0.6931 (mmp80) REVERT: B 327 ARG cc_start: 0.7667 (ptp90) cc_final: 0.7359 (mtt180) REVERT: B 363 ARG cc_start: 0.7773 (tpp80) cc_final: 0.7536 (ttm-80) REVERT: C 170 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7721 (ttm-80) REVERT: C 253 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7298 (tt0) REVERT: C 262 GLN cc_start: 0.8102 (mp10) cc_final: 0.7876 (mp10) REVERT: E 143 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7716 (tptt) REVERT: E 401 ASP cc_start: 0.8024 (t70) cc_final: 0.7772 (t0) REVERT: E 406 GLN cc_start: 0.8079 (mt0) cc_final: 0.7823 (tt0) REVERT: E 575 LYS cc_start: 0.7293 (mmmt) cc_final: 0.7032 (mtmt) REVERT: E 615 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8652 (mp) REVERT: E 624 ASP cc_start: 0.8187 (t0) cc_final: 0.7873 (t0) REVERT: E 626 ARG cc_start: 0.8752 (tpp-160) cc_final: 0.8540 (tpp-160) REVERT: F 94 ASN cc_start: 0.8241 (p0) cc_final: 0.7914 (p0) REVERT: G 79 ARG cc_start: 0.7559 (tpp-160) cc_final: 0.7294 (mmp80) REVERT: G 163 GLU cc_start: 0.7794 (mp0) cc_final: 0.7232 (mp0) REVERT: G 178 LYS cc_start: 0.7846 (ptmt) cc_final: 0.7594 (pttm) outliers start: 50 outliers final: 39 residues processed: 291 average time/residue: 0.7786 time to fit residues: 253.7622 Evaluate side-chains 302 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 283 optimal weight: 2.9990 chunk 245 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 281 optimal weight: 0.6980 chunk 260 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 285 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN B 94 ASN C 72 GLN C 218 GLN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 HIS H 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.108279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081548 restraints weight = 47065.363| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.21 r_work: 0.3193 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24139 Z= 0.115 Angle : 0.520 7.463 32902 Z= 0.260 Chirality : 0.038 0.145 3651 Planarity : 0.004 0.048 4239 Dihedral : 4.900 70.795 3433 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.72 % Allowed : 12.95 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.16), residues: 2957 helix: 2.66 (0.15), residues: 1223 sheet: 1.39 (0.20), residues: 670 loop : -0.02 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 210 TYR 0.016 0.001 TYR G 67 PHE 0.030 0.002 PHE A 624 TRP 0.018 0.001 TRP C 244 HIS 0.010 0.001 HIS E 670 Details of bonding type rmsd covalent geometry : bond 0.00257 (24121) covalent geometry : angle 0.51731 (32860) SS BOND : bond 0.00208 ( 12) SS BOND : angle 0.82121 ( 24) hydrogen bonds : bond 0.04213 ( 1343) hydrogen bonds : angle 4.20832 ( 3999) link_BETA1-4 : bond 0.00334 ( 2) link_BETA1-4 : angle 1.11661 ( 6) link_NAG-ASN : bond 0.00268 ( 4) link_NAG-ASN : angle 2.38957 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11297.32 seconds wall clock time: 192 minutes 23.66 seconds (11543.66 seconds total)