Starting phenix.real_space_refine on Fri May 16 10:59:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p7w_17537/05_2025/8p7w_17537.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p7w_17537/05_2025/8p7w_17537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p7w_17537/05_2025/8p7w_17537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p7w_17537/05_2025/8p7w_17537.map" model { file = "/net/cci-nas-00/data/ceres_data/8p7w_17537/05_2025/8p7w_17537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p7w_17537/05_2025/8p7w_17537.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 9232 2.51 5 N 2392 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14380 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4509 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 19, 'TRANS': 559} Chain breaks: 3 Chain: "B" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4509 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 19, 'TRANS': 559} Chain breaks: 3 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Y" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Time building chain proxies: 9.77, per 1000 atoms: 0.68 Number of scatterers: 14380 At special positions: 0 Unit cell: (93.24, 91.56, 183.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 2678 8.00 N 2392 7.00 C 9232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 106 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 50 " - pdb=" SG CYS Y 106 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.9 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3376 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 38.2% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.906A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 removed outlier: 3.619A pdb=" N PHE A 117 " --> pdb=" O PRO A 114 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS A 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER A 121 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.518A pdb=" N LYS A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 4.050A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.837A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.651A pdb=" N LYS A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.580A pdb=" N LEU A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.556A pdb=" N LEU A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.825A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 413 removed outlier: 3.898A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 440 removed outlier: 3.615A pdb=" N THR A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.621A pdb=" N VAL A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 446 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 447 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 465 through 476 removed outlier: 3.724A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 removed outlier: 3.844A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.514A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 528 removed outlier: 3.699A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.541A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 650 removed outlier: 5.076A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.904A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.617A pdb=" N PHE B 117 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 121 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.500A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 removed outlier: 3.534A pdb=" N LYS B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 removed outlier: 4.036A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 200 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 234 removed outlier: 4.098A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 3.654A pdb=" N LYS B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.630A pdb=" N LEU B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.576A pdb=" N LEU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.823A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN B 391 " --> pdb=" O ASN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 413 removed outlier: 3.819A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 removed outlier: 3.595A pdb=" N THR B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 447 removed outlier: 3.600A pdb=" N VAL B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 446 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 465 through 476 removed outlier: 3.727A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 494 removed outlier: 3.867A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix Processing helix chain 'B' and resid 502 through 528 removed outlier: 3.684A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.574A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 571 Processing helix chain 'B' and resid 572 through 586 Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 650 removed outlier: 5.073A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.107A pdb=" N TYR C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'Y' and resid 28 through 32 removed outlier: 4.046A pdb=" N TYR Y 31 " --> pdb=" O THR Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 109 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 71 removed outlier: 5.560A pdb=" N SER A 65 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N TYR A 44 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY A 69 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N HIS A 40 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET A 71 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER A 38 " --> pdb=" O MET A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.386A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 76 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 255 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 310 removed outlier: 4.080A pdb=" N ARG A 309 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 71 removed outlier: 5.473A pdb=" N SER B 65 " --> pdb=" O TYR B 44 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TYR B 44 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLY B 69 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N HIS B 40 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET B 71 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N SER B 38 " --> pdb=" O MET B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.375A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN B 76 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 255 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.813A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.588A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.588A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 49 removed outlier: 6.458A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.764A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.764A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'G' and resid 44 through 48 removed outlier: 6.421A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.845A pdb=" N SER Y 71 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 46 through 49 removed outlier: 7.078A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1746 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: 4.67 Time building geometry restraints manager: 4.27 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: 4530 1.34 - 1.46: 3605 1.46 - 1.58: 6445 1.58 - 1.70: 0 1.70 - 1.81: 118 Bond restraints: 14698 Sorted by residual: bond pdb=" CG PRO D 88 " pdb=" CD PRO D 88 " ideal model delta sigma weight residual 1.503 1.552 -0.049 3.40e-02 8.65e+02 2.04e+00 bond pdb=" C CYS A 592 " pdb=" O CYS A 592 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.87e+00 bond pdb=" C CYS B 592 " pdb=" O CYS B 592 " ideal model delta sigma weight residual 1.249 1.237 0.011 8.50e-03 1.38e+04 1.81e+00 bond pdb=" CA ARG C 67 " pdb=" CB ARG C 67 " ideal model delta sigma weight residual 1.526 1.546 -0.020 1.51e-02 4.39e+03 1.69e+00 bond pdb=" CG1 ILE B 412 " pdb=" CD1 ILE B 412 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 ... (remaining 14693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 19635 2.40 - 4.79: 241 4.79 - 7.19: 36 7.19 - 9.58: 1 9.58 - 11.98: 3 Bond angle restraints: 19916 Sorted by residual: angle pdb=" N GLU B 458 " pdb=" CA GLU B 458 " pdb=" CB GLU B 458 " ideal model delta sigma weight residual 110.12 115.83 -5.71 1.47e+00 4.63e-01 1.51e+01 angle pdb=" C SER B 572 " pdb=" N ILE B 573 " pdb=" CA ILE B 573 " ideal model delta sigma weight residual 120.33 123.34 -3.01 8.00e-01 1.56e+00 1.42e+01 angle pdb=" C SER A 572 " pdb=" N ILE A 573 " pdb=" CA ILE A 573 " ideal model delta sigma weight residual 120.33 123.34 -3.01 8.00e-01 1.56e+00 1.41e+01 angle pdb=" CB MET Y 83 " pdb=" CG MET Y 83 " pdb=" SD MET Y 83 " ideal model delta sigma weight residual 112.70 123.85 -11.15 3.00e+00 1.11e-01 1.38e+01 angle pdb=" C TYR D 60 " pdb=" N ASN D 61 " pdb=" CA ASN D 61 " ideal model delta sigma weight residual 120.49 125.58 -5.09 1.42e+00 4.96e-01 1.28e+01 ... (remaining 19911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7471 17.71 - 35.42: 950 35.42 - 53.14: 191 53.14 - 70.85: 29 70.85 - 88.56: 16 Dihedral angle restraints: 8657 sinusoidal: 3355 harmonic: 5302 Sorted by residual: dihedral pdb=" CB CYS G 23 " pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " pdb=" CB CYS G 88 " ideal model delta sinusoidal sigma weight residual 93.00 138.05 -45.05 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS Y 50 " pdb=" SG CYS Y 50 " pdb=" SG CYS Y 106 " pdb=" CB CYS Y 106 " ideal model delta sinusoidal sigma weight residual 93.00 54.71 38.29 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CB CYS C 50 " pdb=" SG CYS C 50 " pdb=" SG CYS C 106 " pdb=" CB CYS C 106 " ideal model delta sinusoidal sigma weight residual 93.00 57.95 35.05 1 1.00e+01 1.00e-02 1.74e+01 ... (remaining 8654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1222 0.029 - 0.058: 701 0.058 - 0.087: 216 0.087 - 0.116: 80 0.116 - 0.145: 29 Chirality restraints: 2248 Sorted by residual: chirality pdb=" CA ILE Y 51 " pdb=" N ILE Y 51 " pdb=" C ILE Y 51 " pdb=" CB ILE Y 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE C 51 " pdb=" N ILE C 51 " pdb=" C ILE C 51 " pdb=" CB ILE C 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA LEU B 140 " pdb=" N LEU B 140 " pdb=" C LEU B 140 " pdb=" CB LEU B 140 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2245 not shown) Planarity restraints: 2508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 87 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO D 88 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 90 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ASP F 90 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP F 90 " 0.013 2.00e-02 2.50e+03 pdb=" N THR F 91 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 68 " 0.013 2.00e-02 2.50e+03 1.41e-02 3.46e+00 pdb=" CG PHE C 68 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 68 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 68 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 68 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 68 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 68 " 0.000 2.00e-02 2.50e+03 ... (remaining 2505 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1494 2.74 - 3.28: 13842 3.28 - 3.82: 23824 3.82 - 4.36: 27027 4.36 - 4.90: 48398 Nonbonded interactions: 114585 Sorted by model distance: nonbonded pdb=" OG1 THR D 23 " pdb=" OE1 GLN D 78 " model vdw 2.206 3.040 nonbonded pdb=" O ASN C 103 " pdb=" OH TYR C 109 " model vdw 2.217 3.040 nonbonded pdb=" O LEU C 11 " pdb=" OG1 THR C 121 " model vdw 2.219 3.040 nonbonded pdb=" O SER G 77 " pdb=" OG SER G 77 " model vdw 2.221 3.040 nonbonded pdb=" O ASN Y 103 " pdb=" OH TYR Y 109 " model vdw 2.229 3.040 ... (remaining 114580 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'Y' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 5.940 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 35.890 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 : 0.004 0.053 14709 Z= 0.182 Angle : 0.723 11.978 19938 Z= 0.424 Chirality : 0.042 0.145 2248 Planarity : 0.004 0.101 2508 Dihedral : 15.985 88.560 5248 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.45 % Allowed : 23.09 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.20), residues: 1824 helix: 1.05 (0.21), residues: 652 sheet: -1.48 (0.24), residues: 390 loop : -2.46 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 36 HIS 0.009 0.001 HIS A 155 PHE 0.032 0.001 PHE C 68 TYR 0.012 0.001 TYR B 463 ARG 0.006 0.001 ARG Y 101 Details of bonding type rmsd hydrogen bonds : bond 0.16552 ( 627) hydrogen bonds : angle 5.68047 ( 1746) SS BOND : bond 0.00345 ( 11) SS BOND : angle 1.12501 ( 22) covalent geometry : bond 0.00381 (14698) covalent geometry : angle 0.72253 (19916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 382 time to evaluate : 1.567 Fit side-chains REVERT: B 393 GLN cc_start: 0.7833 (pp30) cc_final: 0.7587 (mt0) REVERT: B 481 MET cc_start: 0.8443 (tpp) cc_final: 0.8227 (mmm) REVERT: D 77 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7804 (t0) REVERT: D 78 GLN cc_start: 0.8200 (mt0) cc_final: 0.7522 (mp10) REVERT: F 13 LYS cc_start: 0.7672 (mtpp) cc_final: 0.7203 (ptmm) REVERT: F 70 ILE cc_start: 0.8305 (mm) cc_final: 0.8076 (mt) REVERT: F 77 ASN cc_start: 0.8889 (t0) cc_final: 0.8663 (t0) REVERT: F 78 GLN cc_start: 0.7901 (pt0) cc_final: 0.7451 (pt0) REVERT: F 111 GLN cc_start: 0.7305 (mp10) cc_final: 0.7081 (mp10) REVERT: G 17 ASP cc_start: 0.7813 (m-30) cc_final: 0.7431 (m-30) outliers start: 7 outliers final: 1 residues processed: 385 average time/residue: 0.2754 time to fit residues: 152.1112 Evaluate side-chains 360 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 358 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain D residue 77 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN G 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107816 restraints weight = 20062.485| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.73 r_work: 0.3172 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14709 Z= 0.154 Angle : 0.560 8.012 19938 Z= 0.290 Chirality : 0.040 0.145 2248 Planarity : 0.004 0.070 2508 Dihedral : 3.951 35.390 2004 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.07 % Allowed : 19.15 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.20), residues: 1824 helix: 1.50 (0.21), residues: 652 sheet: -1.30 (0.26), residues: 372 loop : -2.41 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 36 HIS 0.006 0.001 HIS A 155 PHE 0.018 0.001 PHE A 293 TYR 0.014 0.001 TYR B 463 ARG 0.005 0.000 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 627) hydrogen bonds : angle 4.48415 ( 1746) SS BOND : bond 0.00358 ( 11) SS BOND : angle 1.23247 ( 22) covalent geometry : bond 0.00359 (14698) covalent geometry : angle 0.55879 (19916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 373 time to evaluate : 1.689 Fit side-chains revert: symmetry clash REVERT: A 398 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7808 (mt0) REVERT: A 417 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8397 (mmmm) REVERT: A 541 MET cc_start: 0.8190 (mtm) cc_final: 0.7826 (ttm) REVERT: B 292 ASP cc_start: 0.8669 (m-30) cc_final: 0.8430 (m-30) REVERT: B 311 GLU cc_start: 0.7391 (mp0) cc_final: 0.7097 (mp0) REVERT: D 103 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8234 (mmtt) REVERT: E 11 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: F 13 LYS cc_start: 0.7670 (mtpp) cc_final: 0.7194 (ptmm) REVERT: F 78 GLN cc_start: 0.8009 (pt0) cc_final: 0.7612 (pm20) REVERT: G 17 ASP cc_start: 0.7798 (m-30) cc_final: 0.7443 (m-30) REVERT: Y 77 ASN cc_start: 0.8383 (t0) cc_final: 0.8174 (t0) outliers start: 64 outliers final: 29 residues processed: 402 average time/residue: 0.2596 time to fit residues: 150.7616 Evaluate side-chains 378 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 347 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 33 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 123 optimal weight: 5.9990 chunk 22 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN D 78 GLN E 6 GLN F 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110650 restraints weight = 20066.376| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.75 r_work: 0.3207 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14709 Z= 0.107 Angle : 0.516 7.142 19938 Z= 0.266 Chirality : 0.039 0.135 2248 Planarity : 0.003 0.062 2508 Dihedral : 3.666 20.396 2000 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.37 % Allowed : 20.29 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1824 helix: 1.72 (0.21), residues: 652 sheet: -1.01 (0.28), residues: 336 loop : -2.31 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 35 HIS 0.005 0.001 HIS A 155 PHE 0.020 0.001 PHE Y 68 TYR 0.013 0.001 TYR B 463 ARG 0.004 0.000 ARG C 101 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 627) hydrogen bonds : angle 4.16049 ( 1746) SS BOND : bond 0.00264 ( 11) SS BOND : angle 0.95967 ( 22) covalent geometry : bond 0.00245 (14698) covalent geometry : angle 0.51571 (19916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 372 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 292 ASP cc_start: 0.8657 (m-30) cc_final: 0.8447 (m-30) REVERT: A 398 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7710 (mt0) REVERT: A 502 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8848 (mmtm) REVERT: B 43 CYS cc_start: 0.6732 (m) cc_final: 0.6297 (m) REVERT: B 292 ASP cc_start: 0.8651 (m-30) cc_final: 0.8420 (m-30) REVERT: B 446 GLU cc_start: 0.8626 (mp0) cc_final: 0.7952 (mp0) REVERT: D 107 ASP cc_start: 0.8796 (m-30) cc_final: 0.8488 (m-30) REVERT: E 11 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6451 (m-80) REVERT: F 13 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7160 (ptmm) REVERT: F 78 GLN cc_start: 0.7994 (pt0) cc_final: 0.7575 (pm20) REVERT: G 17 ASP cc_start: 0.7877 (m-30) cc_final: 0.7556 (m-30) REVERT: Y 73 ASP cc_start: 0.8628 (t0) cc_final: 0.8329 (t0) REVERT: Y 77 ASN cc_start: 0.8373 (t0) cc_final: 0.8169 (t0) outliers start: 53 outliers final: 33 residues processed: 395 average time/residue: 0.2626 time to fit residues: 150.9939 Evaluate side-chains 387 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 352 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 119 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 176 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN F 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107301 restraints weight = 19993.897| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.73 r_work: 0.3166 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14709 Z= 0.142 Angle : 0.540 8.446 19938 Z= 0.276 Chirality : 0.040 0.147 2248 Planarity : 0.004 0.057 2508 Dihedral : 3.735 20.186 2000 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 4.64 % Allowed : 19.34 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1824 helix: 1.77 (0.21), residues: 654 sheet: -0.98 (0.27), residues: 340 loop : -2.24 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 37 HIS 0.004 0.001 HIS A 155 PHE 0.016 0.001 PHE A 293 TYR 0.015 0.001 TYR B 336 ARG 0.005 0.000 ARG Y 101 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 627) hydrogen bonds : angle 4.08919 ( 1746) SS BOND : bond 0.00338 ( 11) SS BOND : angle 0.99174 ( 22) covalent geometry : bond 0.00334 (14698) covalent geometry : angle 0.53937 (19916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 369 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 ASP cc_start: 0.8660 (m-30) cc_final: 0.8420 (m-30) REVERT: A 398 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: A 402 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8476 (t) REVERT: B 131 MET cc_start: 0.8169 (ttm) cc_final: 0.7937 (ttm) REVERT: B 292 ASP cc_start: 0.8652 (m-30) cc_final: 0.8440 (m-30) REVERT: B 398 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: B 446 GLU cc_start: 0.8661 (mp0) cc_final: 0.8000 (mp0) REVERT: C 73 ASP cc_start: 0.8509 (t0) cc_final: 0.8274 (t0) REVERT: D 78 GLN cc_start: 0.8329 (mt0) cc_final: 0.7889 (mt0) REVERT: D 81 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7729 (tp) REVERT: D 107 ASP cc_start: 0.8836 (m-30) cc_final: 0.8560 (m-30) REVERT: E 11 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: F 78 GLN cc_start: 0.8133 (pt0) cc_final: 0.7685 (pm20) REVERT: G 17 ASP cc_start: 0.7833 (m-30) cc_final: 0.7531 (m-30) REVERT: Y 77 ASN cc_start: 0.8405 (t0) cc_final: 0.8194 (t0) outliers start: 73 outliers final: 50 residues processed: 404 average time/residue: 0.2918 time to fit residues: 172.4271 Evaluate side-chains 405 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 350 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN F 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104080 restraints weight = 20120.525| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.72 r_work: 0.3118 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14709 Z= 0.203 Angle : 0.587 9.877 19938 Z= 0.303 Chirality : 0.042 0.165 2248 Planarity : 0.004 0.055 2508 Dihedral : 3.951 20.330 2000 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.79 % Allowed : 19.15 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1824 helix: 1.77 (0.21), residues: 652 sheet: -0.83 (0.27), residues: 360 loop : -2.26 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 37 HIS 0.004 0.001 HIS A 583 PHE 0.018 0.002 PHE D 79 TYR 0.015 0.002 TYR B 463 ARG 0.005 0.001 ARG Y 101 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 627) hydrogen bonds : angle 4.17326 ( 1746) SS BOND : bond 0.00400 ( 11) SS BOND : angle 1.14213 ( 22) covalent geometry : bond 0.00474 (14698) covalent geometry : angle 0.58619 (19916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 373 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8753 (m110) cc_final: 0.8147 (t0) REVERT: A 148 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8954 (mp) REVERT: A 292 ASP cc_start: 0.8756 (m-30) cc_final: 0.8514 (m-30) REVERT: A 398 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: A 402 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8476 (t) REVERT: B 292 ASP cc_start: 0.8765 (m-30) cc_final: 0.8545 (m-30) REVERT: B 398 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7937 (mt0) REVERT: C 73 ASP cc_start: 0.8639 (t0) cc_final: 0.8417 (t0) REVERT: D 81 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7970 (tp) REVERT: D 107 ASP cc_start: 0.8910 (m-30) cc_final: 0.8662 (m-30) REVERT: E 11 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.6573 (m-80) REVERT: E 24 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6526 (mtmm) REVERT: F 13 LYS cc_start: 0.7997 (mtpp) cc_final: 0.7421 (ptmm) REVERT: F 78 GLN cc_start: 0.8218 (pt0) cc_final: 0.7803 (pm20) REVERT: G 17 ASP cc_start: 0.8033 (m-30) cc_final: 0.7676 (m-30) REVERT: Y 73 ASP cc_start: 0.8647 (t0) cc_final: 0.8297 (t0) REVERT: Y 77 ASN cc_start: 0.8436 (t0) cc_final: 0.8203 (t0) outliers start: 91 outliers final: 59 residues processed: 417 average time/residue: 0.2591 time to fit residues: 157.2949 Evaluate side-chains 429 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 363 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 106 optimal weight: 0.0270 chunk 143 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104074 restraints weight = 20169.061| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.72 r_work: 0.3118 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14709 Z= 0.186 Angle : 0.592 9.994 19938 Z= 0.301 Chirality : 0.042 0.155 2248 Planarity : 0.004 0.054 2508 Dihedral : 3.987 21.268 2000 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 5.41 % Allowed : 20.23 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1824 helix: 1.96 (0.21), residues: 636 sheet: -0.80 (0.26), residues: 360 loop : -2.25 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 37 HIS 0.004 0.001 HIS A 583 PHE 0.017 0.001 PHE A 293 TYR 0.021 0.001 TYR B 463 ARG 0.005 0.000 ARG Y 101 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 627) hydrogen bonds : angle 4.12053 ( 1746) SS BOND : bond 0.00377 ( 11) SS BOND : angle 1.09351 ( 22) covalent geometry : bond 0.00439 (14698) covalent geometry : angle 0.59107 (19916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 371 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8747 (m110) cc_final: 0.8146 (t0) REVERT: A 398 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7724 (mt0) REVERT: A 402 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8500 (t) REVERT: A 446 GLU cc_start: 0.8822 (mp0) cc_final: 0.8168 (mp0) REVERT: B 292 ASP cc_start: 0.8768 (m-30) cc_final: 0.8561 (m-30) REVERT: B 398 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: B 446 GLU cc_start: 0.8843 (mp0) cc_final: 0.8213 (mp0) REVERT: C 73 ASP cc_start: 0.8649 (t0) cc_final: 0.8367 (t0) REVERT: D 13 LYS cc_start: 0.7596 (mtpp) cc_final: 0.7168 (ptmm) REVERT: D 81 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8057 (tp) REVERT: D 107 ASP cc_start: 0.8941 (m-30) cc_final: 0.8705 (m-30) REVERT: E 11 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.6571 (m-80) REVERT: F 78 GLN cc_start: 0.8233 (pt0) cc_final: 0.7819 (pm20) REVERT: G 17 ASP cc_start: 0.8045 (m-30) cc_final: 0.7687 (m-30) REVERT: Y 73 ASP cc_start: 0.8688 (t0) cc_final: 0.8463 (t0) REVERT: Y 77 ASN cc_start: 0.8424 (t0) cc_final: 0.8198 (t0) outliers start: 85 outliers final: 63 residues processed: 408 average time/residue: 0.2614 time to fit residues: 155.2217 Evaluate side-chains 439 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 371 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104076 restraints weight = 20104.229| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.72 r_work: 0.3119 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14709 Z= 0.179 Angle : 0.600 9.284 19938 Z= 0.305 Chirality : 0.042 0.156 2248 Planarity : 0.004 0.053 2508 Dihedral : 3.986 20.987 2000 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.28 % Allowed : 20.87 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1824 helix: 1.98 (0.21), residues: 636 sheet: -0.76 (0.27), residues: 360 loop : -2.20 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 35 HIS 0.003 0.001 HIS A 583 PHE 0.017 0.001 PHE D 79 TYR 0.028 0.001 TYR B 463 ARG 0.005 0.000 ARG Y 101 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 627) hydrogen bonds : angle 4.08962 ( 1746) SS BOND : bond 0.00376 ( 11) SS BOND : angle 1.16181 ( 22) covalent geometry : bond 0.00423 (14698) covalent geometry : angle 0.59929 (19916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 386 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8732 (m110) cc_final: 0.7926 (t0) REVERT: A 398 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: A 402 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8497 (t) REVERT: B 105 ASP cc_start: 0.7943 (t70) cc_final: 0.7718 (t70) REVERT: B 292 ASP cc_start: 0.8798 (m-30) cc_final: 0.8587 (m-30) REVERT: B 295 LEU cc_start: 0.9172 (mm) cc_final: 0.8969 (mm) REVERT: B 458 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: C 73 ASP cc_start: 0.8630 (t0) cc_final: 0.8358 (t0) REVERT: D 81 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8093 (tp) REVERT: D 107 ASP cc_start: 0.8916 (m-30) cc_final: 0.8692 (m-30) REVERT: E 11 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: E 24 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6485 (mtmm) REVERT: F 13 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7470 (ptmm) REVERT: F 77 ASN cc_start: 0.8831 (t0) cc_final: 0.8604 (t0) REVERT: F 78 GLN cc_start: 0.8268 (pt0) cc_final: 0.7812 (pm20) REVERT: G 17 ASP cc_start: 0.8102 (m-30) cc_final: 0.7744 (m-30) REVERT: Y 73 ASP cc_start: 0.8746 (t0) cc_final: 0.8533 (t0) REVERT: Y 77 ASN cc_start: 0.8396 (t0) cc_final: 0.8170 (t0) outliers start: 83 outliers final: 60 residues processed: 421 average time/residue: 0.2585 time to fit residues: 158.7774 Evaluate side-chains 435 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 369 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 172 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104540 restraints weight = 20058.598| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.71 r_work: 0.3126 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14709 Z= 0.165 Angle : 0.591 10.603 19938 Z= 0.302 Chirality : 0.041 0.184 2248 Planarity : 0.004 0.052 2508 Dihedral : 3.967 21.137 2000 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.64 % Allowed : 21.82 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1824 helix: 2.00 (0.21), residues: 636 sheet: -0.65 (0.26), residues: 392 loop : -2.15 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 35 HIS 0.003 0.001 HIS B 267 PHE 0.016 0.001 PHE A 293 TYR 0.022 0.001 TYR B 463 ARG 0.009 0.000 ARG C 101 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 627) hydrogen bonds : angle 4.04543 ( 1746) SS BOND : bond 0.00355 ( 11) SS BOND : angle 1.19530 ( 22) covalent geometry : bond 0.00389 (14698) covalent geometry : angle 0.59032 (19916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 381 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8714 (m110) cc_final: 0.8118 (t0) REVERT: A 398 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7813 (mt0) REVERT: A 402 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8497 (t) REVERT: B 105 ASP cc_start: 0.7921 (t70) cc_final: 0.7694 (t70) REVERT: B 295 LEU cc_start: 0.9171 (mm) cc_final: 0.8958 (mm) REVERT: B 446 GLU cc_start: 0.8809 (mp0) cc_final: 0.8188 (mp0) REVERT: B 458 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: C 73 ASP cc_start: 0.8636 (t0) cc_final: 0.8351 (t0) REVERT: D 13 LYS cc_start: 0.7760 (mtpp) cc_final: 0.7193 (ptmm) REVERT: D 81 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8149 (tp) REVERT: D 107 ASP cc_start: 0.8899 (m-30) cc_final: 0.8653 (m-30) REVERT: E 11 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: E 24 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6484 (mtmm) REVERT: F 13 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7473 (ptmm) REVERT: F 77 ASN cc_start: 0.8844 (t0) cc_final: 0.8603 (t0) REVERT: F 78 GLN cc_start: 0.8280 (pt0) cc_final: 0.7841 (pm20) REVERT: G 17 ASP cc_start: 0.8123 (m-30) cc_final: 0.7784 (m-30) REVERT: Y 77 ASN cc_start: 0.8373 (t0) cc_final: 0.8147 (t0) outliers start: 73 outliers final: 59 residues processed: 412 average time/residue: 0.2574 time to fit residues: 154.6016 Evaluate side-chains 439 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 374 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 106 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.139896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106619 restraints weight = 19843.374| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.71 r_work: 0.3153 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14709 Z= 0.133 Angle : 0.586 9.399 19938 Z= 0.298 Chirality : 0.041 0.222 2248 Planarity : 0.004 0.051 2508 Dihedral : 3.873 20.548 2000 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.07 % Allowed : 22.65 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1824 helix: 2.04 (0.21), residues: 636 sheet: -0.51 (0.26), residues: 392 loop : -2.08 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 35 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.001 PHE A 293 TYR 0.019 0.001 TYR B 463 ARG 0.009 0.000 ARG C 101 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 627) hydrogen bonds : angle 3.92718 ( 1746) SS BOND : bond 0.00305 ( 11) SS BOND : angle 1.09151 ( 22) covalent geometry : bond 0.00315 (14698) covalent geometry : angle 0.58511 (19916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 388 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8682 (m110) cc_final: 0.7905 (t0) REVERT: B 105 ASP cc_start: 0.7899 (t70) cc_final: 0.7663 (t70) REVERT: B 295 LEU cc_start: 0.9134 (mm) cc_final: 0.8919 (mm) REVERT: B 446 GLU cc_start: 0.8854 (mp0) cc_final: 0.8190 (mp0) REVERT: C 73 ASP cc_start: 0.8612 (t0) cc_final: 0.8314 (t0) REVERT: D 13 LYS cc_start: 0.7782 (mtpp) cc_final: 0.7188 (ptmm) REVERT: D 86 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8180 (p) REVERT: E 11 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: F 13 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7389 (ptmm) REVERT: F 77 ASN cc_start: 0.8850 (t0) cc_final: 0.8605 (t0) REVERT: F 78 GLN cc_start: 0.8186 (pt0) cc_final: 0.7750 (pm20) REVERT: G 17 ASP cc_start: 0.8096 (m-30) cc_final: 0.7766 (m-30) outliers start: 64 outliers final: 49 residues processed: 419 average time/residue: 0.2662 time to fit residues: 162.1392 Evaluate side-chains 435 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 384 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 118 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 176 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 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 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105779 restraints weight = 20056.549| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.72 r_work: 0.3139 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14709 Z= 0.149 Angle : 0.610 10.821 19938 Z= 0.309 Chirality : 0.041 0.246 2248 Planarity : 0.004 0.051 2508 Dihedral : 3.895 20.362 2000 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.44 % Allowed : 23.60 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1824 helix: 2.05 (0.21), residues: 636 sheet: -0.46 (0.26), residues: 376 loop : -2.07 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 35 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.001 PHE D 79 TYR 0.021 0.001 TYR B 463 ARG 0.010 0.000 ARG Y 101 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 627) hydrogen bonds : angle 3.93231 ( 1746) SS BOND : bond 0.00341 ( 11) SS BOND : angle 1.22569 ( 22) covalent geometry : bond 0.00354 (14698) covalent geometry : angle 0.60885 (19916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 386 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8701 (m110) cc_final: 0.7909 (t0) REVERT: B 295 LEU cc_start: 0.9134 (mm) cc_final: 0.8916 (mm) REVERT: B 446 GLU cc_start: 0.8864 (mp0) cc_final: 0.8270 (mp0) REVERT: C 73 ASP cc_start: 0.8635 (t0) cc_final: 0.8329 (t0) REVERT: D 13 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7184 (ptmm) REVERT: D 86 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8220 (p) REVERT: E 11 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.6784 (m-80) REVERT: F 77 ASN cc_start: 0.8882 (t0) cc_final: 0.8629 (t0) REVERT: F 78 GLN cc_start: 0.8235 (pt0) cc_final: 0.7759 (pm20) REVERT: G 17 ASP cc_start: 0.8115 (m-30) cc_final: 0.7786 (m-30) REVERT: Y 73 ASP cc_start: 0.8527 (t0) cc_final: 0.8304 (t0) outliers start: 54 outliers final: 45 residues processed: 411 average time/residue: 0.2576 time to fit residues: 154.4888 Evaluate side-chains 424 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 377 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 165 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Y 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.139429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106200 restraints weight = 20048.105| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.71 r_work: 0.3146 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14709 Z= 0.141 Angle : 0.599 10.674 19938 Z= 0.304 Chirality : 0.041 0.247 2248 Planarity : 0.004 0.051 2508 Dihedral : 3.878 20.076 2000 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.31 % Allowed : 23.92 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1824 helix: 2.09 (0.21), residues: 636 sheet: -0.48 (0.26), residues: 392 loop : -2.05 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 35 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.001 PHE A 293 TYR 0.018 0.001 TYR B 336 ARG 0.010 0.000 ARG Y 101 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 627) hydrogen bonds : angle 3.88265 ( 1746) SS BOND : bond 0.00323 ( 11) SS BOND : angle 1.15206 ( 22) covalent geometry : bond 0.00336 (14698) covalent geometry : angle 0.59815 (19916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8204.93 seconds wall clock time: 142 minutes 34.81 seconds (8554.81 seconds total)