Starting phenix.real_space_refine on Wed Jun 11 06:59:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hco_0196/06_2025/6hco_0196_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hco_0196/06_2025/6hco_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/cci-nas-00/data/ceres_data/6hco_0196/06_2025/6hco_0196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hco_0196/06_2025/6hco_0196.map" model { file = "/net/cci-nas-00/data/ceres_data/6hco_0196/06_2025/6hco_0196_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hco_0196/06_2025/6hco_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.33, per 1000 atoms: 0.68 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: 2.97 Conformation dependent library (CDL) restraints added in 1.6 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: 1.44 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: 3.65 Time building geometry restraints manager: 3.51 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: 3.560 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.600 Find NCS groups from input model: 0.450 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- 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 12624 Z= 0.428 Angle : 1.054 17.718 17121 Z= 0.547 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01175 ( 2) link_NAG-ASN : angle 2.80975 ( 6) link_BETA1-4 : bond 0.01625 ( 2) link_BETA1-4 : angle 5.80710 ( 6) hydrogen bonds : bond 0.27384 ( 486) hydrogen bonds : angle 9.79857 ( 1461) SS BOND : bond 0.00537 ( 7) SS BOND : angle 2.28045 ( 14) covalent geometry : bond 0.00941 (12613) covalent geometry : angle 1.04623 (17095) *********************** 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 to be fit. rotamer outliers: 6 poor density : 249 time to evaluate : 1.557 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: 0.2535 time to fit residues: 90.7925 Evaluate side-chains 129 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.082767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.066044 restraints weight = 56624.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.067803 restraints weight = 27967.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.068904 restraints weight = 17130.532| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 12624 Z= 0.149 Angle : 0.733 10.502 17121 Z= 0.370 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 : 12.34 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 2) link_NAG-ASN : angle 2.41515 ( 6) link_BETA1-4 : bond 0.00645 ( 2) link_BETA1-4 : angle 2.54254 ( 6) hydrogen bonds : bond 0.04620 ( 486) hydrogen bonds : angle 5.74656 ( 1461) SS BOND : bond 0.00392 ( 7) SS BOND : angle 0.55363 ( 14) covalent geometry : bond 0.00326 (12613) covalent geometry : angle 0.73048 (17095) *********************** 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 to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.647 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: 0.8461 (mtt) cc_final: 0.8101 (mtm) REVERT: A 207 LEU cc_start: 0.9480 (mp) cc_final: 0.9066 (tp) REVERT: A 470 PHE cc_start: 0.8578 (t80) cc_final: 0.8354 (t80) REVERT: A 496 MET cc_start: 0.7258 (ttm) cc_final: 0.7038 (ttm) REVERT: A 514 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8682 (mpp) REVERT: A 636 MET cc_start: 0.8528 (mtp) cc_final: 0.7872 (mmt) REVERT: A 642 THR cc_start: 0.9342 (m) cc_final: 0.9105 (p) REVERT: B 198 MET cc_start: 0.8790 (mtp) cc_final: 0.8567 (mtt) REVERT: B 228 LEU cc_start: 0.9225 (mt) cc_final: 0.8580 (pp) REVERT: B 490 THR cc_start: 0.8080 (m) cc_final: 0.7334 (m) REVERT: B 510 MET cc_start: 0.8236 (tpp) cc_final: 0.7971 (mmt) outliers start: 32 outliers final: 15 residues processed: 167 average time/residue: 0.2377 time to fit residues: 61.9826 Evaluate side-chains 130 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 514 MET 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 10 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 0.0000 chunk 50 optimal weight: 0.3980 chunk 104 optimal weight: 20.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN ** B 387 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 = 0.3881 r_free = 0.3881 target = 0.081880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.064965 restraints weight = 57198.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.066708 restraints weight = 27925.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.067776 restraints weight = 17160.732| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12624 Z= 0.121 Angle : 0.660 13.111 17121 Z= 0.324 Chirality : 0.042 0.200 1958 Planarity : 0.004 0.043 2130 Dihedral : 6.287 89.462 1817 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.16 % Allowed : 10.27 % Favored : 87.57 % 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: -2.08 (0.21), residues: 1552 helix: -0.58 (0.19), residues: 640 sheet: -1.90 (0.30), residues: 288 loop : -1.82 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 37 HIS 0.003 0.001 HIS A 350 PHE 0.022 0.001 PHE A 578 TYR 0.012 0.001 TYR A 413 ARG 0.005 0.000 ARG A 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00014 ( 2) link_NAG-ASN : angle 1.82737 ( 6) link_BETA1-4 : bond 0.00686 ( 2) link_BETA1-4 : angle 2.60285 ( 6) hydrogen bonds : bond 0.04114 ( 486) hydrogen bonds : angle 5.19805 ( 1461) SS BOND : bond 0.00294 ( 7) SS BOND : angle 0.49010 ( 14) covalent geometry : bond 0.00263 (12613) covalent geometry : angle 0.65721 (17095) *********************** 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 159 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.631 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: 0.8047 (mmt) cc_final: 0.7481 (mmp) REVERT: A 198 MET cc_start: 0.8484 (mtt) cc_final: 0.8135 (mtm) REVERT: A 207 LEU cc_start: 0.9544 (mp) cc_final: 0.9053 (tt) REVERT: A 441 SER cc_start: 0.9078 (m) cc_final: 0.8433 (t) REVERT: A 514 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8712 (mpp) REVERT: A 540 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9122 (mt) REVERT: A 636 MET cc_start: 0.8552 (mtp) cc_final: 0.7934 (mmt) REVERT: B 71 MET cc_start: 0.8383 (mmm) cc_final: 0.7596 (mmp) REVERT: B 228 LEU cc_start: 0.9175 (mt) cc_final: 0.8763 (pp) REVERT: B 231 MET cc_start: 0.8917 (mtp) cc_final: 0.8681 (mtm) REVERT: B 540 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9227 (mt) outliers start: 29 outliers final: 14 residues processed: 146 average time/residue: 0.2595 time to fit residues: 60.0174 Evaluate side-chains 128 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE 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 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 92 VAL Chi-restraints excluded: chain B residue 161 ILE 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 540 LEU Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 119 optimal weight: 7.9990 chunk 104 optimal weight: 0.0980 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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 629 ASN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.075512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057378 restraints weight = 57224.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.058868 restraints weight = 28442.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.059805 restraints weight = 17952.542| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12624 Z= 0.229 Angle : 0.741 8.585 17121 Z= 0.368 Chirality : 0.045 0.173 1958 Planarity : 0.005 0.066 2130 Dihedral : 6.259 84.205 1817 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.75 % Allowed : 11.24 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1552 helix: -0.22 (0.20), residues: 654 sheet: -1.50 (0.31), residues: 274 loop : -1.40 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 624 HIS 0.018 0.002 HIS A 155 PHE 0.024 0.002 PHE F 79 TYR 0.017 0.002 TYR A 570 ARG 0.006 0.001 ARG A 163 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 2) link_NAG-ASN : angle 1.60272 ( 6) link_BETA1-4 : bond 0.00438 ( 2) link_BETA1-4 : angle 3.08130 ( 6) hydrogen bonds : bond 0.03924 ( 486) hydrogen bonds : angle 5.02900 ( 1461) SS BOND : bond 0.00538 ( 7) SS BOND : angle 0.81600 ( 14) covalent geometry : bond 0.00513 (12613) covalent geometry : angle 0.73807 (17095) *********************** 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 151 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 1.410 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: 0.8239 (mmt) cc_final: 0.7817 (mmp) REVERT: A 164 VAL cc_start: 0.9306 (t) cc_final: 0.9099 (m) REVERT: A 228 LEU cc_start: 0.9145 (mt) cc_final: 0.8498 (pp) REVERT: A 540 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9263 (mm) REVERT: B 131 MET cc_start: 0.3239 (OUTLIER) cc_final: 0.3014 (ttt) REVERT: B 486 SER cc_start: 0.8722 (m) cc_final: 0.8265 (t) outliers start: 37 outliers final: 19 residues processed: 136 average time/residue: 0.2245 time to fit residues: 48.5781 Evaluate side-chains 120 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 90 LEU 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 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 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 92 VAL Chi-restraints excluded: chain B residue 131 MET 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 525 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 88 optimal weight: 0.0170 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.076409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058452 restraints weight = 56974.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.060009 restraints weight = 27908.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.060972 restraints weight = 17375.378| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12624 Z= 0.128 Angle : 0.654 10.751 17121 Z= 0.318 Chirality : 0.043 0.263 1958 Planarity : 0.004 0.043 2130 Dihedral : 5.886 86.195 1817 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.53 % Allowed : 11.68 % Favored : 85.79 % 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: -1.18 (0.22), residues: 1552 helix: 0.00 (0.20), residues: 652 sheet: -1.26 (0.32), residues: 274 loop : -1.27 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 624 HIS 0.003 0.001 HIS B 155 PHE 0.019 0.001 PHE A 578 TYR 0.011 0.001 TYR E 91 ARG 0.005 0.001 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00064 ( 2) link_NAG-ASN : angle 1.49004 ( 6) link_BETA1-4 : bond 0.00797 ( 2) link_BETA1-4 : angle 2.33464 ( 6) hydrogen bonds : bond 0.03575 ( 486) hydrogen bonds : angle 4.76147 ( 1461) SS BOND : bond 0.00393 ( 7) SS BOND : angle 0.58447 ( 14) covalent geometry : bond 0.00286 (12613) covalent geometry : angle 0.65201 (17095) *********************** 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 143 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8288 (mmt) cc_final: 0.7913 (mmp) REVERT: A 228 LEU cc_start: 0.9106 (mt) cc_final: 0.8479 (pp) REVERT: B 131 MET cc_start: 0.2777 (OUTLIER) cc_final: 0.2326 (ttt) REVERT: B 228 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8659 (pp) REVERT: B 486 SER cc_start: 0.8696 (m) cc_final: 0.8273 (t) outliers start: 34 outliers final: 22 residues processed: 132 average time/residue: 0.1920 time to fit residues: 40.9876 Evaluate side-chains 121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 33 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 21 ILE 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 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 151 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 484 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 43 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 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** D 111 GLN F 40 GLN ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.072716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.054702 restraints weight = 58312.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.056156 restraints weight = 28870.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.057035 restraints weight = 18180.307| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12624 Z= 0.240 Angle : 0.742 10.622 17121 Z= 0.366 Chirality : 0.045 0.281 1958 Planarity : 0.005 0.051 2130 Dihedral : 6.046 81.244 1817 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.12 % Allowed : 11.24 % Favored : 85.64 % 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: -1.01 (0.22), residues: 1552 helix: 0.10 (0.20), residues: 652 sheet: -1.10 (0.32), residues: 274 loop : -1.16 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 624 HIS 0.007 0.001 HIS B 583 PHE 0.024 0.002 PHE F 79 TYR 0.021 0.002 TYR A 494 ARG 0.005 0.001 ARG B 163 Details of bonding type rmsd link_NAG-ASN : bond 0.00003 ( 2) link_NAG-ASN : angle 1.84141 ( 6) link_BETA1-4 : bond 0.00774 ( 2) link_BETA1-4 : angle 2.89132 ( 6) hydrogen bonds : bond 0.03853 ( 486) hydrogen bonds : angle 4.87455 ( 1461) SS BOND : bond 0.00589 ( 7) SS BOND : angle 1.17080 ( 14) covalent geometry : bond 0.00538 (12613) covalent geometry : angle 0.73905 (17095) *********************** 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 129 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8275 (mmt) cc_final: 0.7977 (mmp) REVERT: A 486 SER cc_start: 0.8854 (m) cc_final: 0.8505 (t) REVERT: A 540 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9266 (mm) REVERT: B 131 MET cc_start: 0.2749 (mtp) cc_final: 0.2268 (ttt) REVERT: B 133 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6210 (t) REVERT: B 228 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8546 (pp) REVERT: B 484 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9037 (pp) REVERT: B 486 SER cc_start: 0.8645 (m) cc_final: 0.8310 (t) REVERT: B 510 MET cc_start: 0.8569 (mmm) cc_final: 0.8062 (tpp) outliers start: 42 outliers final: 26 residues processed: 119 average time/residue: 0.2228 time to fit residues: 42.6503 Evaluate side-chains 110 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 195 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 490 THR 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 C residue 30 LEU 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 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 195 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 123 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN A 601 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** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN B 601 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.067652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.049914 restraints weight = 59357.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051222 restraints weight = 29437.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052048 restraints weight = 18515.488| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.091 12624 Z= 0.453 Angle : 0.955 12.256 17121 Z= 0.478 Chirality : 0.053 0.336 1958 Planarity : 0.006 0.049 2130 Dihedral : 6.869 75.335 1817 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.42 % Allowed : 12.20 % 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: -1.42 (0.22), residues: 1552 helix: -0.27 (0.19), residues: 646 sheet: -1.16 (0.32), residues: 264 loop : -1.43 (0.27), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 624 HIS 0.005 0.002 HIS B 630 PHE 0.034 0.003 PHE F 79 TYR 0.031 0.003 TYR B 494 ARG 0.007 0.001 ARG B 163 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 2) link_NAG-ASN : angle 2.55561 ( 6) link_BETA1-4 : bond 0.00518 ( 2) link_BETA1-4 : angle 3.82284 ( 6) hydrogen bonds : bond 0.04862 ( 486) hydrogen bonds : angle 5.55298 ( 1461) SS BOND : bond 0.00655 ( 7) SS BOND : angle 1.52611 ( 14) covalent geometry : bond 0.00986 (12613) covalent geometry : angle 0.95079 (17095) *********************** 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 124 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 78 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8378 (mmt) cc_final: 0.8029 (mmp) REVERT: A 486 SER cc_start: 0.8977 (m) cc_final: 0.8501 (t) REVERT: A 540 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9408 (mm) REVERT: B 199 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7567 (tm-30) REVERT: B 486 SER cc_start: 0.8807 (m) cc_final: 0.8407 (t) outliers start: 46 outliers final: 30 residues processed: 117 average time/residue: 0.3253 time to fit residues: 62.9117 Evaluate side-chains 98 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 153 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 490 THR 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 33 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 94 THR 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 83 VAL 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 125 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 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 484 LEU Chi-restraints excluded: chain B residue 490 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 27 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 149 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 143 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.070448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052731 restraints weight = 57724.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.054144 restraints weight = 28072.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055014 restraints weight = 17446.511| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12624 Z= 0.168 Angle : 0.705 11.823 17121 Z= 0.349 Chirality : 0.045 0.256 1958 Planarity : 0.004 0.046 2130 Dihedral : 6.177 78.505 1817 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.53 % Allowed : 12.87 % 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: -0.85 (0.22), residues: 1552 helix: 0.23 (0.20), residues: 640 sheet: -0.81 (0.33), residues: 264 loop : -1.15 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 624 HIS 0.003 0.001 HIS B 267 PHE 0.020 0.002 PHE A 578 TYR 0.011 0.002 TYR A 654 ARG 0.003 0.001 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 1.90834 ( 6) link_BETA1-4 : bond 0.00822 ( 2) link_BETA1-4 : angle 2.72416 ( 6) hydrogen bonds : bond 0.03845 ( 486) hydrogen bonds : angle 4.97356 ( 1461) SS BOND : bond 0.00496 ( 7) SS BOND : angle 1.38135 ( 14) covalent geometry : bond 0.00377 (12613) covalent geometry : angle 0.70155 (17095) *********************** 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 115 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8329 (mmt) cc_final: 0.7990 (mmp) REVERT: A 486 SER cc_start: 0.8901 (m) cc_final: 0.8455 (t) REVERT: A 510 MET cc_start: 0.8594 (mmm) cc_final: 0.8314 (tpt) REVERT: A 540 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9344 (mm) REVERT: B 199 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7398 (tm-30) REVERT: B 228 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8578 (pp) REVERT: B 484 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9004 (pp) REVERT: B 486 SER cc_start: 0.8618 (m) cc_final: 0.8248 (t) outliers start: 34 outliers final: 23 residues processed: 107 average time/residue: 0.1953 time to fit residues: 33.9452 Evaluate side-chains 102 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 161 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 490 THR 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 33 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 33 LEU 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 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 153 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 525 LEU 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 74 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 110 optimal weight: 0.0060 chunk 81 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.072647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.055115 restraints weight = 57212.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.056520 restraints weight = 27913.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.057421 restraints weight = 17347.764| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12624 Z= 0.127 Angle : 0.687 11.528 17121 Z= 0.333 Chirality : 0.044 0.255 1958 Planarity : 0.004 0.044 2130 Dihedral : 5.803 79.086 1817 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.71 % Allowed : 14.14 % 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: -0.56 (0.22), residues: 1552 helix: 0.61 (0.20), residues: 640 sheet: -0.64 (0.32), residues: 274 loop : -1.18 (0.27), residues: 638 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 0.019 0.001 PHE B 448 TYR 0.012 0.001 TYR B 469 ARG 0.005 0.001 ARG F 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00024 ( 2) link_NAG-ASN : angle 1.72810 ( 6) link_BETA1-4 : bond 0.00705 ( 2) link_BETA1-4 : angle 2.34291 ( 6) hydrogen bonds : bond 0.03542 ( 486) hydrogen bonds : angle 4.78620 ( 1461) SS BOND : bond 0.00342 ( 7) SS BOND : angle 1.00697 ( 14) covalent geometry : bond 0.00289 (12613) covalent geometry : angle 0.68491 (17095) *********************** 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 107 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8271 (mmt) cc_final: 0.7957 (mmp) REVERT: A 486 SER cc_start: 0.8943 (m) cc_final: 0.8477 (t) REVERT: B 71 MET cc_start: 0.8478 (mmm) cc_final: 0.7683 (mmp) REVERT: B 199 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7324 (tm-30) REVERT: B 228 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8549 (pp) REVERT: B 484 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9010 (pp) REVERT: B 486 SER cc_start: 0.8686 (m) cc_final: 0.8234 (t) outliers start: 23 outliers final: 17 residues processed: 101 average time/residue: 0.1995 time to fit residues: 32.7848 Evaluate side-chains 97 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 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 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 94 THR Chi-restraints excluded: chain F residue 86 VAL 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 228 LEU Chi-restraints excluded: chain B residue 484 LEU 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 91 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 0.0270 chunk 148 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.072238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.054773 restraints weight = 56712.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056204 restraints weight = 28064.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.057070 restraints weight = 17311.868| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12624 Z= 0.145 Angle : 0.676 11.861 17121 Z= 0.331 Chirality : 0.044 0.241 1958 Planarity : 0.004 0.045 2130 Dihedral : 5.693 76.897 1817 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.79 % Allowed : 13.91 % 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: -0.34 (0.22), residues: 1552 helix: 0.78 (0.20), residues: 642 sheet: -0.50 (0.33), residues: 272 loop : -1.07 (0.27), residues: 638 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 0.016 0.001 PHE A 578 TYR 0.010 0.001 TYR B 459 ARG 0.005 0.000 ARG B 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 2) link_NAG-ASN : angle 1.67528 ( 6) link_BETA1-4 : bond 0.00763 ( 2) link_BETA1-4 : angle 2.41399 ( 6) hydrogen bonds : bond 0.03475 ( 486) hydrogen bonds : angle 4.75174 ( 1461) SS BOND : bond 0.00327 ( 7) SS BOND : angle 0.89030 ( 14) covalent geometry : bond 0.00334 (12613) covalent geometry : angle 0.67388 (17095) ********************** 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 100 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8215 (mmt) cc_final: 0.7930 (mmp) REVERT: A 486 SER cc_start: 0.9014 (m) cc_final: 0.8603 (t) REVERT: A 540 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9278 (mp) REVERT: B 199 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7407 (tm-30) REVERT: B 228 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8536 (pp) REVERT: B 484 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8989 (pp) REVERT: B 486 SER cc_start: 0.8707 (m) cc_final: 0.8443 (t) outliers start: 24 outliers final: 20 residues processed: 93 average time/residue: 0.1921 time to fit residues: 29.4452 Evaluate side-chains 99 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 483 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 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 94 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 490 THR 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 112 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.071717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.054226 restraints weight = 57634.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055644 restraints weight = 28538.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056498 restraints weight = 17588.834| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12624 Z= 0.173 Angle : 0.688 11.961 17121 Z= 0.336 Chirality : 0.044 0.240 1958 Planarity : 0.004 0.045 2130 Dihedral : 5.704 74.453 1817 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.93 % Allowed : 14.06 % Favored : 84.00 % 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: -0.21 (0.22), residues: 1552 helix: 0.90 (0.21), residues: 642 sheet: -0.39 (0.33), residues: 272 loop : -1.03 (0.27), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 624 HIS 0.002 0.001 HIS B 375 PHE 0.017 0.002 PHE D 79 TYR 0.013 0.001 TYR A 494 ARG 0.004 0.000 ARG F 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 2) link_NAG-ASN : angle 1.69843 ( 6) link_BETA1-4 : bond 0.00699 ( 2) link_BETA1-4 : angle 2.45537 ( 6) hydrogen bonds : bond 0.03519 ( 486) hydrogen bonds : angle 4.76937 ( 1461) SS BOND : bond 0.00354 ( 7) SS BOND : angle 0.93312 ( 14) covalent geometry : bond 0.00393 (12613) covalent geometry : angle 0.68537 (17095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4066.31 seconds wall clock time: 74 minutes 21.53 seconds (4461.53 seconds total)