Starting phenix.real_space_refine on Thu Sep 26 07:59:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/09_2024/6hco_0196_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/09_2024/6hco_0196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/09_2024/6hco_0196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/09_2024/6hco_0196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/09_2024/6hco_0196_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/09_2024/6hco_0196_neut.cif" } resolution = 3.58 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= 0.004 sd= 0.041 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 69 5.16 5 C 7960 2.51 5 N 2032 2.21 5 O 2277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12338 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4379 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 18, 'TRANS': 544} Chain breaks: 3 Chain: "C" 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: "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: "B" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4379 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 18, 'TRANS': 544} Chain breaks: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'FY5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.43, per 1000 atoms: 0.60 Number of scatterers: 12338 At special positions: 0 Unit cell: (101.5, 93.38, 142.912, 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 69 16.00 O 2277 8.00 N 2032 7.00 C 7960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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 C 23 " - pdb=" SG CYS C 88 " 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=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 596 " " NAG H 1 " - " ASN B 596 " Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 16 sheets defined 44.0% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.926A pdb=" N ASP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 153 through 163 removed outlier: 4.198A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.768A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 232 removed outlier: 3.731A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.091A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.729A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.638A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 390 removed outlier: 3.665A pdb=" N SER A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.611A pdb=" N VAL A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 441 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.100A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 465 through 477 removed outlier: 4.015A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 484 through 498 removed outlier: 4.222A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 497 " --> pdb=" O VAL A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 529 removed outlier: 3.781A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 550 removed outlier: 3.569A pdb=" N LEU A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.666A pdb=" N ILE A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.559A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.779A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 650 removed outlier: 3.808A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.664A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.663A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.927A pdb=" N ASP B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 153 through 163 removed outlier: 4.266A pdb=" N ILE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.501A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.742A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 232 removed outlier: 3.708A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 271 through 280 removed outlier: 4.181A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.754A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.639A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 removed outlier: 3.668A pdb=" N SER B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 413 removed outlier: 3.667A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 444 through 451 removed outlier: 4.075A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 465 through 477 removed outlier: 4.017A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 Processing helix chain 'B' and resid 484 through 498 removed outlier: 4.226A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 497 " --> pdb=" O VAL B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 529 removed outlier: 3.698A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 550 removed outlier: 3.587A pdb=" N LEU B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 546 " --> pdb=" O THR B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.689A pdb=" N ILE B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.554A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.776A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 578 " --> pdb=" O PRO B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 650 removed outlier: 3.835A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71 removed outlier: 3.629A pdb=" N GLY A 69 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS A 40 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.062A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 241 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU A 75 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 268 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 258 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.590A pdb=" N TYR C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.426A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'D' and resid 19 through 23 removed outlier: 3.653A pdb=" N PHE D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 60 removed outlier: 4.864A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 34 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 58 through 60 removed outlier: 4.864A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 34 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.590A pdb=" N TYR E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.426A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'F' and resid 19 through 23 removed outlier: 3.654A pdb=" N PHE F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 58 through 60 removed outlier: 4.864A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 34 " --> pdb=" O PHE F 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 58 through 60 removed outlier: 4.864A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 34 " --> pdb=" O PHE F 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.648A pdb=" N GLY B 69 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS B 40 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.057A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 207 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N SER B 241 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU B 209 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 268 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 258 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1461 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: 3.47 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1935 1.30 - 1.43: 3507 1.43 - 1.56: 7058 1.56 - 1.68: 7 1.68 - 1.81: 106 Bond restraints: 12613 Sorted by residual: bond pdb=" C02 FY5 A1003 " pdb=" C10 FY5 A1003 " ideal model delta sigma weight residual 1.518 1.328 0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" C04 FY5 A1003 " pdb=" C05 FY5 A1003 " ideal model delta sigma weight residual 1.527 1.667 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C07 FY5 A1003 " pdb=" C08 FY5 A1003 " ideal model delta sigma weight residual 1.527 1.397 0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C02 FY5 A1003 " pdb=" C07 FY5 A1003 " ideal model delta sigma weight residual 1.533 1.650 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" N ASN B 436 " pdb=" CA ASN B 436 " ideal model delta sigma weight residual 1.459 1.398 0.061 1.17e-02 7.31e+03 2.72e+01 ... (remaining 12608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 16891 3.54 - 7.09: 169 7.09 - 10.63: 30 10.63 - 14.17: 2 14.17 - 17.72: 3 Bond angle restraints: 17095 Sorted by residual: angle pdb=" N ASN B 436 " pdb=" CA ASN B 436 " pdb=" C ASN B 436 " ideal model delta sigma weight residual 110.97 102.48 8.49 1.09e+00 8.42e-01 6.07e+01 angle pdb=" N ASN A 436 " pdb=" CA ASN A 436 " pdb=" C ASN A 436 " ideal model delta sigma weight residual 110.97 102.58 8.39 1.09e+00 8.42e-01 5.92e+01 angle pdb=" C THR A 435 " pdb=" N ASN A 436 " pdb=" CA ASN A 436 " ideal model delta sigma weight residual 120.65 110.74 9.91 1.32e+00 5.74e-01 5.63e+01 angle pdb=" C THR B 435 " pdb=" N ASN B 436 " pdb=" CA ASN B 436 " ideal model delta sigma weight residual 120.65 110.91 9.74 1.32e+00 5.74e-01 5.45e+01 angle pdb=" O22 FY5 A1003 " pdb=" S21 FY5 A1003 " pdb=" O23 FY5 A1003 " ideal model delta sigma weight residual 115.34 97.62 17.72 3.00e+00 1.11e-01 3.49e+01 ... (remaining 17090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7186 17.89 - 35.78: 251 35.78 - 53.67: 52 53.67 - 71.56: 4 71.56 - 89.44: 9 Dihedral angle restraints: 7502 sinusoidal: 2986 harmonic: 4516 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 16.14 76.86 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CA GLY F 43 " pdb=" C GLY F 43 " pdb=" N LYS F 44 " pdb=" CA LYS F 44 " ideal model delta harmonic sigma weight residual -180.00 -149.39 -30.61 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA GLY D 43 " pdb=" C GLY D 43 " pdb=" N LYS D 44 " pdb=" CA LYS D 44 " ideal model delta harmonic sigma weight residual -180.00 -149.40 -30.60 0 5.00e+00 4.00e-02 3.75e+01 ... (remaining 7499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1279 0.053 - 0.106: 538 0.106 - 0.159: 120 0.159 - 0.212: 15 0.212 - 0.265: 6 Chirality restraints: 1958 Sorted by residual: chirality pdb=" CA THR E 94 " pdb=" N THR E 94 " pdb=" C THR E 94 " pdb=" CB THR E 94 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA THR C 94 " pdb=" N THR C 94 " pdb=" C THR C 94 " pdb=" CB THR C 94 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C05 FY5 A1003 " pdb=" C04 FY5 A1003 " pdb=" C06 FY5 A1003 " pdb=" C15 FY5 A1003 " both_signs ideal model delta sigma weight residual False 2.38 2.62 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1955 not shown) Planarity restraints: 2132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 63 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ILE B 63 " -0.066 2.00e-02 2.50e+03 pdb=" O ILE B 63 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 64 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 63 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ILE A 63 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE A 63 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 64 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 98 " 0.006 2.00e-02 2.50e+03 1.94e-02 6.57e+00 pdb=" CG PHE E 98 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE E 98 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE E 98 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE E 98 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE E 98 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 98 " -0.005 2.00e-02 2.50e+03 ... (remaining 2129 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 211 2.65 - 3.21: 11362 3.21 - 3.77: 19326 3.77 - 4.34: 26890 4.34 - 4.90: 43396 Nonbonded interactions: 101185 Sorted by model distance: nonbonded pdb=" O PHE B 431 " pdb=" CG2 THR B 435 " model vdw 2.082 3.460 nonbonded pdb=" O PHE A 431 " pdb=" CG2 THR A 435 " model vdw 2.108 3.460 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.185 3.040 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR E 36 " pdb=" OE1 GLN E 89 " model vdw 2.267 3.040 ... (remaining 101180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 35 through 654) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.940 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.009 0.190 12613 Z= 0.590 Angle : 1.046 17.718 17095 Z= 0.545 Chirality : 0.058 0.265 1958 Planarity : 0.007 0.057 2130 Dihedral : 10.572 89.444 4597 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.45 % Allowed : 4.02 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.59 (0.17), residues: 1552 helix: -3.41 (0.13), residues: 578 sheet: -2.92 (0.27), residues: 274 loop : -2.60 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP E 96 HIS 0.015 0.004 HIS A 583 PHE 0.040 0.004 PHE E 98 TYR 0.028 0.004 TYR B 570 ARG 0.011 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 249 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ILE cc_start: 0.8807 (mt) cc_final: 0.8583 (mm) REVERT: A 207 LEU cc_start: 0.9286 (mp) cc_final: 0.8830 (tt) REVERT: A 251 LYS cc_start: 0.7555 (pttt) cc_final: 0.7203 (tptp) REVERT: A 441 SER cc_start: 0.8983 (m) cc_final: 0.8076 (t) REVERT: A 636 MET cc_start: 0.8160 (mtp) cc_final: 0.7728 (mmt) REVERT: F 53 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7871 (t0) outliers start: 6 outliers final: 2 residues processed: 252 average time/residue: 0.2390 time to fit residues: 85.7536 Evaluate side-chains 129 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain B residue 435 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 68 ASN A 116 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 425 ASN A 436 ASN A 437 GLN A 583 HIS D 16 GLN D 77 ASN F 53 ASN F 77 ASN B 41 ASN B 68 ASN B 109 ASN B 116 ASN ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 425 ASN B 436 ASN B 437 GLN B 582 GLN B 583 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12613 Z= 0.207 Angle : 0.730 10.503 17095 Z= 0.369 Chirality : 0.045 0.230 1958 Planarity : 0.005 0.050 2130 Dihedral : 6.911 85.741 1821 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.38 % Allowed : 8.26 % Favored : 89.36 % 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: -2.74 (0.20), residues: 1552 helix: -1.19 (0.18), residues: 608 sheet: -2.20 (0.30), residues: 272 loop : -2.12 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 564 HIS 0.004 0.001 HIS A 350 PHE 0.024 0.002 PHE A 250 TYR 0.017 0.002 TYR A 342 ARG 0.005 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8464 (mtt) cc_final: 0.8142 (mtm) REVERT: A 207 LEU cc_start: 0.9415 (mp) cc_final: 0.9013 (tp) REVERT: A 251 LYS cc_start: 0.7602 (pttt) cc_final: 0.7392 (pptt) REVERT: A 470 PHE cc_start: 0.8438 (t80) cc_final: 0.8187 (t80) REVERT: A 636 MET cc_start: 0.8198 (mtp) cc_final: 0.7711 (mmt) REVERT: A 642 THR cc_start: 0.9201 (m) cc_final: 0.8980 (p) REVERT: B 198 MET cc_start: 0.8814 (mtp) cc_final: 0.8587 (mtt) REVERT: B 228 LEU cc_start: 0.9114 (mt) cc_final: 0.8438 (pp) REVERT: B 490 THR cc_start: 0.7776 (m) cc_final: 0.7098 (m) REVERT: B 510 MET cc_start: 0.8022 (tpp) cc_final: 0.7812 (mmt) outliers start: 32 outliers final: 15 residues processed: 167 average time/residue: 0.2091 time to fit residues: 53.7694 Evaluate side-chains 130 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 635 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 582 GLN D 111 GLN E 37 GLN F 5 GLN B 629 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 12613 Z= 0.479 Angle : 0.894 15.876 17095 Z= 0.445 Chirality : 0.049 0.204 1958 Planarity : 0.006 0.050 2130 Dihedral : 6.913 83.623 1817 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.12 % Allowed : 10.19 % Favored : 86.68 % 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: -1.84 (0.21), residues: 1552 helix: -0.58 (0.19), residues: 648 sheet: -1.70 (0.32), residues: 264 loop : -1.54 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 624 HIS 0.006 0.001 HIS B 583 PHE 0.028 0.003 PHE A 578 TYR 0.031 0.003 TYR C 36 ARG 0.008 0.001 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 104 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8053 (mmt) cc_final: 0.7754 (mmp) REVERT: A 207 LEU cc_start: 0.9446 (mp) cc_final: 0.9078 (tt) REVERT: A 228 LEU cc_start: 0.9123 (mt) cc_final: 0.8906 (mt) REVERT: A 342 TYR cc_start: 0.8160 (t80) cc_final: 0.7886 (t80) REVERT: A 486 SER cc_start: 0.8583 (m) cc_final: 0.8204 (t) REVERT: A 510 MET cc_start: 0.8422 (mmm) cc_final: 0.8071 (mmm) REVERT: A 523 MET cc_start: 0.8686 (tmm) cc_final: 0.8468 (tmm) REVERT: A 540 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9233 (mm) REVERT: E 24 LYS cc_start: 0.8740 (tptp) cc_final: 0.8446 (tppt) REVERT: E 70 ASP cc_start: 0.8492 (m-30) cc_final: 0.7715 (m-30) REVERT: B 486 SER cc_start: 0.8602 (m) cc_final: 0.8138 (t) REVERT: B 523 MET cc_start: 0.8735 (tmm) cc_final: 0.8503 (tmm) outliers start: 42 outliers final: 22 residues processed: 135 average time/residue: 0.1966 time to fit residues: 41.7700 Evaluate side-chains 110 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 519 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12613 Z= 0.217 Angle : 0.676 10.708 17095 Z= 0.333 Chirality : 0.043 0.184 1958 Planarity : 0.004 0.051 2130 Dihedral : 6.199 84.273 1817 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.16 % Allowed : 12.13 % Favored : 85.71 % 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: -1.33 (0.22), residues: 1552 helix: -0.10 (0.20), residues: 648 sheet: -1.38 (0.32), residues: 264 loop : -1.35 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 624 HIS 0.003 0.001 HIS A 350 PHE 0.025 0.002 PHE A 578 TYR 0.012 0.001 TYR E 91 ARG 0.005 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8067 (mmt) cc_final: 0.7814 (mmp) REVERT: A 164 VAL cc_start: 0.9269 (t) cc_final: 0.9066 (m) REVERT: A 207 LEU cc_start: 0.9443 (mp) cc_final: 0.9056 (tt) REVERT: A 228 LEU cc_start: 0.9064 (mt) cc_final: 0.8402 (pp) REVERT: A 540 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9220 (mm) REVERT: B 486 SER cc_start: 0.8523 (m) cc_final: 0.8050 (t) REVERT: B 510 MET cc_start: 0.8436 (tpp) cc_final: 0.8229 (tpp) outliers start: 29 outliers final: 19 residues processed: 122 average time/residue: 0.2080 time to fit residues: 40.7505 Evaluate side-chains 103 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN A 601 ASN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN F 40 GLN ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 12613 Z= 0.494 Angle : 0.830 13.112 17095 Z= 0.413 Chirality : 0.047 0.180 1958 Planarity : 0.005 0.050 2130 Dihedral : 6.404 78.358 1817 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.05 % Allowed : 12.35 % Favored : 84.60 % 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: -1.25 (0.22), residues: 1552 helix: -0.06 (0.20), residues: 642 sheet: -1.22 (0.32), residues: 264 loop : -1.32 (0.27), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 624 HIS 0.008 0.001 HIS B 583 PHE 0.031 0.002 PHE D 79 TYR 0.025 0.002 TYR A 494 ARG 0.006 0.001 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 82 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8084 (mmt) cc_final: 0.7811 (mmp) REVERT: A 342 TYR cc_start: 0.8190 (t80) cc_final: 0.7818 (t80) REVERT: A 486 SER cc_start: 0.8742 (m) cc_final: 0.8393 (t) REVERT: A 540 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9301 (mm) REVERT: B 133 THR cc_start: 0.6518 (OUTLIER) cc_final: 0.6315 (t) REVERT: B 486 SER cc_start: 0.8639 (m) cc_final: 0.8154 (t) outliers start: 41 outliers final: 27 residues processed: 116 average time/residue: 0.1870 time to fit residues: 35.1295 Evaluate side-chains 102 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN B 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12613 Z= 0.187 Angle : 0.662 9.972 17095 Z= 0.326 Chirality : 0.043 0.184 1958 Planarity : 0.004 0.047 2130 Dihedral : 5.857 79.706 1817 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.46 % Allowed : 13.24 % Favored : 84.30 % 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: -0.93 (0.22), residues: 1552 helix: 0.20 (0.20), residues: 650 sheet: -0.92 (0.32), residues: 274 loop : -1.24 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 624 HIS 0.002 0.001 HIS B 267 PHE 0.021 0.001 PHE A 578 TYR 0.011 0.001 TYR C 87 ARG 0.004 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 92 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8069 (mmt) cc_final: 0.7782 (mmp) REVERT: A 486 SER cc_start: 0.8590 (m) cc_final: 0.8346 (t) REVERT: A 540 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9227 (mp) REVERT: B 133 THR cc_start: 0.5995 (OUTLIER) cc_final: 0.5743 (t) REVERT: B 486 SER cc_start: 0.8486 (m) cc_final: 0.8107 (t) outliers start: 33 outliers final: 23 residues processed: 114 average time/residue: 0.1900 time to fit residues: 35.1905 Evaluate side-chains 102 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12613 Z= 0.294 Angle : 0.696 10.532 17095 Z= 0.345 Chirality : 0.044 0.272 1958 Planarity : 0.004 0.047 2130 Dihedral : 5.879 78.650 1817 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.68 % Allowed : 12.95 % Favored : 84.38 % 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: -0.80 (0.22), residues: 1552 helix: 0.27 (0.20), residues: 652 sheet: -0.80 (0.32), residues: 274 loop : -1.14 (0.28), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 624 HIS 0.004 0.001 HIS A 583 PHE 0.019 0.002 PHE D 79 TYR 0.016 0.002 TYR A 494 ARG 0.003 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 78 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8038 (mmt) cc_final: 0.7820 (mmp) REVERT: A 421 THR cc_start: 0.9459 (OUTLIER) cc_final: 0.9256 (t) REVERT: A 486 SER cc_start: 0.8775 (m) cc_final: 0.8418 (t) REVERT: A 540 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9232 (mm) REVERT: B 133 THR cc_start: 0.6317 (OUTLIER) cc_final: 0.6060 (t) REVERT: B 421 THR cc_start: 0.9467 (OUTLIER) cc_final: 0.9257 (t) REVERT: B 486 SER cc_start: 0.8538 (m) cc_final: 0.8065 (t) outliers start: 36 outliers final: 27 residues processed: 105 average time/residue: 0.1834 time to fit residues: 31.6976 Evaluate side-chains 104 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 73 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 0.0270 chunk 116 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12613 Z= 0.226 Angle : 0.650 10.542 17095 Z= 0.322 Chirality : 0.043 0.260 1958 Planarity : 0.004 0.046 2130 Dihedral : 5.706 78.103 1817 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.98 % Allowed : 12.72 % Favored : 84.30 % 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: -0.59 (0.22), residues: 1552 helix: 0.52 (0.20), residues: 648 sheet: -0.63 (0.32), residues: 274 loop : -1.14 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 35 HIS 0.002 0.001 HIS B 267 PHE 0.018 0.001 PHE A 578 TYR 0.011 0.001 TYR C 87 ARG 0.003 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 78 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8029 (mmt) cc_final: 0.7803 (mmp) REVERT: A 486 SER cc_start: 0.8699 (m) cc_final: 0.8468 (t) REVERT: A 540 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9219 (mm) REVERT: B 133 THR cc_start: 0.6297 (OUTLIER) cc_final: 0.6051 (t) REVERT: B 199 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7405 (tm-30) REVERT: B 486 SER cc_start: 0.8523 (m) cc_final: 0.8217 (t) REVERT: B 540 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9220 (mp) outliers start: 40 outliers final: 27 residues processed: 110 average time/residue: 0.2092 time to fit residues: 36.7152 Evaluate side-chains 104 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 74 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 83 optimal weight: 0.0040 chunk 60 optimal weight: 0.0040 chunk 108 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 130 optimal weight: 0.3980 chunk 137 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 overall best weight: 0.6206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12613 Z= 0.156 Angle : 0.635 11.249 17095 Z= 0.310 Chirality : 0.042 0.276 1958 Planarity : 0.004 0.045 2130 Dihedral : 5.515 80.870 1817 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.16 % Allowed : 13.69 % Favored : 84.15 % 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: -0.53 (0.22), residues: 1552 helix: 0.60 (0.20), residues: 654 sheet: -0.50 (0.33), residues: 272 loop : -1.23 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 48 HIS 0.002 0.000 HIS B 267 PHE 0.016 0.001 PHE A 578 TYR 0.010 0.001 TYR C 87 ARG 0.003 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7965 (mmt) cc_final: 0.7752 (mmp) REVERT: A 540 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9205 (mp) REVERT: B 133 THR cc_start: 0.6065 (OUTLIER) cc_final: 0.5816 (t) REVERT: B 486 SER cc_start: 0.8446 (m) cc_final: 0.8062 (t) outliers start: 29 outliers final: 19 residues processed: 108 average time/residue: 0.1906 time to fit residues: 33.6008 Evaluate side-chains 96 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12613 Z= 0.185 Angle : 0.654 11.434 17095 Z= 0.316 Chirality : 0.043 0.304 1958 Planarity : 0.003 0.045 2130 Dihedral : 5.450 78.706 1817 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.71 % Allowed : 14.58 % Favored : 83.71 % 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: -0.42 (0.22), residues: 1552 helix: 0.73 (0.20), residues: 652 sheet: -0.47 (0.32), residues: 276 loop : -1.21 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 35 HIS 0.002 0.001 HIS B 267 PHE 0.015 0.001 PHE A 578 TYR 0.010 0.001 TYR C 87 ARG 0.003 0.000 ARG B 383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7929 (mmt) cc_final: 0.7717 (mmp) REVERT: B 133 THR cc_start: 0.6114 (OUTLIER) cc_final: 0.5858 (t) REVERT: B 199 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7398 (tm-30) REVERT: B 228 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8398 (pp) REVERT: B 231 MET cc_start: 0.8560 (mtm) cc_final: 0.8073 (mtm) REVERT: B 486 SER cc_start: 0.8553 (m) cc_final: 0.8267 (t) outliers start: 23 outliers final: 21 residues processed: 96 average time/residue: 0.1900 time to fit residues: 29.7509 Evaluate side-chains 98 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.069025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.051280 restraints weight = 58628.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.052634 restraints weight = 28736.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.053477 restraints weight = 18105.718| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.6987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12613 Z= 0.423 Angle : 0.768 12.037 17095 Z= 0.383 Chirality : 0.047 0.309 1958 Planarity : 0.004 0.046 2130 Dihedral : 5.940 71.073 1817 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.31 % Allowed : 14.21 % Favored : 83.48 % 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: -0.43 (0.22), residues: 1552 helix: 0.72 (0.20), residues: 640 sheet: -0.43 (0.32), residues: 274 loop : -1.19 (0.27), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 624 HIS 0.003 0.001 HIS B 583 PHE 0.021 0.002 PHE D 79 TYR 0.024 0.002 TYR A 494 ARG 0.010 0.001 ARG F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.73 seconds wall clock time: 39 minutes 16.32 seconds (2356.32 seconds total)