Starting phenix.real_space_refine on Thu Sep 18 00:25:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hco_0196/09_2025/6hco_0196_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hco_0196/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6hco_0196/09_2025/6hco_0196_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hco_0196/09_2025/6hco_0196_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hco_0196/09_2025/6hco_0196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hco_0196/09_2025/6hco_0196.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.98, per 1000 atoms: 0.24 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: 0.95 Conformation dependent library (CDL) restraints added in 512.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.44 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: 1.81 Time building geometry restraints manager: 1.31 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: 3.650 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.830 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG A 96 TYR 0.028 0.004 TYR B 570 PHE 0.040 0.004 PHE E 98 TRP 0.027 0.004 TRP E 96 HIS 0.015 0.004 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00941 (12613) covalent geometry : angle 1.04623 (17095) SS BOND : bond 0.00537 ( 7) SS BOND : angle 2.28045 ( 14) hydrogen bonds : bond 0.27384 ( 486) hydrogen bonds : angle 9.79857 ( 1461) link_BETA1-4 : bond 0.01625 ( 2) link_BETA1-4 : angle 5.80710 ( 6) link_NAG-ASN : bond 0.01175 ( 2) link_NAG-ASN : angle 2.80975 ( 6) *********************** 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 : 0.401 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: 0.8587 (mm) REVERT: A 207 LEU cc_start: 0.9286 (mp) cc_final: 0.8831 (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: 0.1060 time to fit residues: 38.0473 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 : 0.366 ------------------------------------------------------------------------------- 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 98 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 582 GLN A 583 HIS ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN F 53 ASN F 77 ASN B 41 ASN B 68 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.079034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.061347 restraints weight = 57598.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.063007 restraints weight = 28323.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.064014 restraints weight = 17597.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.064639 restraints weight = 12788.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.065011 restraints weight = 10418.591| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12624 Z= 0.213 Angle : 0.782 10.670 17121 Z= 0.395 Chirality : 0.045 0.200 1958 Planarity : 0.005 0.055 2130 Dihedral : 6.972 84.925 1821 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.38 % Allowed : 8.78 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.20), residues: 1552 helix: -1.19 (0.18), residues: 628 sheet: -2.19 (0.30), residues: 274 loop : -1.93 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 163 TYR 0.019 0.002 TYR B 494 PHE 0.026 0.002 PHE B 506 TRP 0.014 0.002 TRP F 37 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00471 (12613) covalent geometry : angle 0.77953 (17095) SS BOND : bond 0.00508 ( 7) SS BOND : angle 0.71878 ( 14) hydrogen bonds : bond 0.04752 ( 486) hydrogen bonds : angle 5.80735 ( 1461) link_BETA1-4 : bond 0.00640 ( 2) link_BETA1-4 : angle 2.70831 ( 6) link_NAG-ASN : bond 0.00337 ( 2) link_NAG-ASN : angle 2.10081 ( 6) *********************** 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 159 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.491 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: 0.8251 (mmt) cc_final: 0.7841 (mmp) REVERT: A 198 MET cc_start: 0.8576 (mtt) cc_final: 0.8239 (mtm) REVERT: A 441 SER cc_start: 0.9099 (m) cc_final: 0.8467 (t) REVERT: A 514 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8756 (mpp) REVERT: A 515 MET cc_start: 0.8784 (mmm) cc_final: 0.8502 (mmm) REVERT: E 33 LEU cc_start: 0.8987 (tm) cc_final: 0.8748 (tm) REVERT: B 164 VAL cc_start: 0.9453 (t) cc_final: 0.9223 (m) REVERT: B 228 LEU cc_start: 0.9254 (mt) cc_final: 0.8618 (pp) REVERT: B 490 THR cc_start: 0.8089 (m) cc_final: 0.7412 (m) REVERT: B 510 MET cc_start: 0.8351 (tpp) cc_final: 0.8079 (tpp) outliers start: 32 outliers final: 16 residues processed: 151 average time/residue: 0.0866 time to fit residues: 20.6403 Evaluate side-chains 127 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 514 MET 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 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 105 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN F 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.072002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.053756 restraints weight = 58844.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.055131 restraints weight = 29335.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.055987 restraints weight = 18611.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.056505 restraints weight = 13874.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056809 restraints weight = 11460.606| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 12624 Z= 0.347 Angle : 0.871 17.631 17121 Z= 0.430 Chirality : 0.048 0.210 1958 Planarity : 0.005 0.051 2130 Dihedral : 6.831 82.627 1817 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.12 % Allowed : 10.94 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.22), residues: 1552 helix: -0.49 (0.19), residues: 658 sheet: -1.74 (0.32), residues: 264 loop : -1.53 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 383 TYR 0.023 0.003 TYR B 494 PHE 0.027 0.003 PHE F 79 TRP 0.019 0.002 TRP B 624 HIS 0.004 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00758 (12613) covalent geometry : angle 0.86747 (17095) SS BOND : bond 0.00667 ( 7) SS BOND : angle 1.22077 ( 14) hydrogen bonds : bond 0.04980 ( 486) hydrogen bonds : angle 5.55530 ( 1461) link_BETA1-4 : bond 0.01116 ( 2) link_BETA1-4 : angle 3.53465 ( 6) link_NAG-ASN : bond 0.00126 ( 2) link_NAG-ASN : angle 2.04543 ( 6) *********************** 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 138 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 0.457 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: 0.8252 (mmt) cc_final: 0.7949 (mmp) REVERT: A 228 LEU cc_start: 0.9193 (mt) cc_final: 0.8478 (pp) REVERT: A 342 TYR cc_start: 0.8279 (t80) cc_final: 0.8029 (t80) REVERT: A 490 THR cc_start: 0.8573 (m) cc_final: 0.8367 (p) REVERT: A 510 MET cc_start: 0.8581 (mmm) cc_final: 0.8167 (mmm) REVERT: A 540 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9334 (mm) REVERT: E 24 LYS cc_start: 0.8746 (tptp) cc_final: 0.8509 (tppt) REVERT: E 54 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8855 (tt) REVERT: E 87 TYR cc_start: 0.8730 (m-80) cc_final: 0.8418 (m-80) REVERT: B 486 SER cc_start: 0.8705 (m) cc_final: 0.8027 (t) REVERT: B 510 MET cc_start: 0.8614 (tpp) cc_final: 0.8310 (tpp) REVERT: B 540 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9295 (mm) outliers start: 42 outliers final: 21 residues processed: 125 average time/residue: 0.0794 time to fit residues: 16.1446 Evaluate side-chains 108 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 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 540 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.074277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.056109 restraints weight = 57341.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.057554 restraints weight = 28060.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.058444 restraints weight = 17636.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.059002 restraints weight = 12992.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.059313 restraints weight = 10682.793| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5286 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= 0.143 Angle : 0.672 12.393 17121 Z= 0.328 Chirality : 0.043 0.183 1958 Planarity : 0.004 0.044 2130 Dihedral : 6.119 84.352 1817 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.16 % Allowed : 12.72 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.22), residues: 1552 helix: -0.02 (0.20), residues: 650 sheet: -1.46 (0.32), residues: 274 loop : -1.29 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 383 TYR 0.012 0.001 TYR E 91 PHE 0.014 0.001 PHE F 79 TRP 0.014 0.001 TRP A 624 HIS 0.003 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00322 (12613) covalent geometry : angle 0.66899 (17095) SS BOND : bond 0.00474 ( 7) SS BOND : angle 1.08844 ( 14) hydrogen bonds : bond 0.03794 ( 486) hydrogen bonds : angle 5.00365 ( 1461) link_BETA1-4 : bond 0.00839 ( 2) link_BETA1-4 : angle 2.50875 ( 6) link_NAG-ASN : bond 0.00095 ( 2) link_NAG-ASN : angle 1.65261 ( 6) *********************** 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 135 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.508 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: 0.8383 (mmt) cc_final: 0.8031 (mmp) REVERT: A 228 LEU cc_start: 0.9149 (mt) cc_final: 0.8519 (pp) REVERT: A 540 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9277 (mm) REVERT: E 87 TYR cc_start: 0.8593 (m-80) cc_final: 0.8320 (m-80) REVERT: F 49 MET cc_start: 0.7942 (mmt) cc_final: 0.7697 (mmt) REVERT: B 484 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8992 (pp) REVERT: B 486 SER cc_start: 0.8628 (m) cc_final: 0.7725 (t) REVERT: B 510 MET cc_start: 0.8692 (tpp) cc_final: 0.8368 (mmm) REVERT: B 540 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9355 (mm) outliers start: 29 outliers final: 19 residues processed: 129 average time/residue: 0.0894 time to fit residues: 18.2415 Evaluate side-chains 107 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 195 SER Chi-restraints excluded: chain A residue 206 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 A residue 646 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 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 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 Chi-restraints excluded: chain B residue 635 CYS Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 95 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 57 optimal weight: 0.0670 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 overall best weight: 3.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 601 ASN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.072127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.054011 restraints weight = 58785.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.055394 restraints weight = 28980.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056260 restraints weight = 18355.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056765 restraints weight = 13569.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057060 restraints weight = 11239.705| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12624 Z= 0.226 Angle : 0.708 11.993 17121 Z= 0.349 Chirality : 0.044 0.194 1958 Planarity : 0.004 0.046 2130 Dihedral : 6.038 81.272 1817 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.90 % Allowed : 12.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.22), residues: 1552 helix: 0.25 (0.21), residues: 650 sheet: -1.22 (0.32), residues: 274 loop : -1.19 (0.28), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 39 TYR 0.016 0.002 TYR A 494 PHE 0.021 0.002 PHE D 79 TRP 0.015 0.002 TRP B 624 HIS 0.004 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00499 (12613) covalent geometry : angle 0.70514 (17095) SS BOND : bond 0.00501 ( 7) SS BOND : angle 0.97925 ( 14) hydrogen bonds : bond 0.03860 ( 486) hydrogen bonds : angle 5.01658 ( 1461) link_BETA1-4 : bond 0.01329 ( 2) link_BETA1-4 : angle 3.02271 ( 6) link_NAG-ASN : bond 0.00068 ( 2) link_NAG-ASN : angle 1.79440 ( 6) *********************** 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 125 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8416 (mp) REVERT: A 71 MET cc_start: 0.8337 (mmt) cc_final: 0.8075 (mmp) REVERT: A 486 SER cc_start: 0.8810 (m) cc_final: 0.8382 (t) REVERT: A 540 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9293 (mm) REVERT: B 63 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 486 SER cc_start: 0.8626 (m) cc_final: 0.7580 (t) REVERT: B 510 MET cc_start: 0.8716 (tpp) cc_final: 0.8356 (mmm) REVERT: B 540 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9339 (mm) outliers start: 39 outliers final: 24 residues processed: 118 average time/residue: 0.0836 time to fit residues: 16.2906 Evaluate side-chains 101 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain C residue 21 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 63 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 635 CYS Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 97 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 40 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 = 0.3701 r_free = 0.3701 target = 0.073696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.055619 restraints weight = 57610.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.057122 restraints weight = 28133.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.058028 restraints weight = 17391.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.058573 restraints weight = 12704.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.058889 restraints weight = 10408.311| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12624 Z= 0.132 Angle : 0.645 9.884 17121 Z= 0.315 Chirality : 0.042 0.189 1958 Planarity : 0.004 0.043 2130 Dihedral : 5.757 81.851 1817 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.75 % Allowed : 12.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.22), residues: 1552 helix: 0.43 (0.21), residues: 652 sheet: -1.00 (0.32), residues: 274 loop : -1.15 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 383 TYR 0.010 0.001 TYR C 91 PHE 0.013 0.001 PHE D 79 TRP 0.013 0.001 TRP B 624 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00303 (12613) covalent geometry : angle 0.64225 (17095) SS BOND : bond 0.00387 ( 7) SS BOND : angle 0.98315 ( 14) hydrogen bonds : bond 0.03499 ( 486) hydrogen bonds : angle 4.77274 ( 1461) link_BETA1-4 : bond 0.00867 ( 2) link_BETA1-4 : angle 2.41835 ( 6) link_NAG-ASN : bond 0.00036 ( 2) link_NAG-ASN : angle 1.54874 ( 6) *********************** 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 128 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8332 (mmt) cc_final: 0.8030 (mmp) REVERT: A 486 SER cc_start: 0.8780 (m) cc_final: 0.8286 (t) REVERT: B 486 SER cc_start: 0.8532 (m) cc_final: 0.7450 (t) REVERT: B 510 MET cc_start: 0.8780 (tpp) cc_final: 0.8342 (mmm) REVERT: B 540 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9309 (mp) outliers start: 37 outliers final: 23 residues processed: 120 average time/residue: 0.0822 time to fit residues: 16.1186 Evaluate side-chains 106 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 206 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 646 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 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 228 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 Chi-restraints excluded: chain B residue 635 CYS 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 83 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 121 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 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 = 0.3680 r_free = 0.3680 target = 0.072639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.054711 restraints weight = 57410.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.056179 restraints weight = 28353.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057035 restraints weight = 17628.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.057547 restraints weight = 12984.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.057848 restraints weight = 10725.504| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12624 Z= 0.168 Angle : 0.658 10.368 17121 Z= 0.324 Chirality : 0.043 0.266 1958 Planarity : 0.004 0.045 2130 Dihedral : 5.696 79.393 1817 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.90 % Allowed : 13.02 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.22), residues: 1552 helix: 0.55 (0.21), residues: 650 sheet: -0.88 (0.32), residues: 274 loop : -1.12 (0.28), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 383 TYR 0.012 0.001 TYR A 494 PHE 0.017 0.001 PHE D 79 TRP 0.013 0.001 TRP D 35 HIS 0.003 0.001 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00379 (12613) covalent geometry : angle 0.65515 (17095) SS BOND : bond 0.00385 ( 7) SS BOND : angle 0.85381 ( 14) hydrogen bonds : bond 0.03481 ( 486) hydrogen bonds : angle 4.74183 ( 1461) link_BETA1-4 : bond 0.00788 ( 2) link_BETA1-4 : angle 2.54497 ( 6) link_NAG-ASN : bond 0.00020 ( 2) link_NAG-ASN : angle 1.63507 ( 6) *********************** 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 125 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8328 (mmt) cc_final: 0.8073 (mmp) REVERT: A 421 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9270 (t) REVERT: A 486 SER cc_start: 0.8797 (m) cc_final: 0.8390 (t) REVERT: A 510 MET cc_start: 0.8614 (mmm) cc_final: 0.8162 (tpp) REVERT: A 540 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9258 (mp) REVERT: B 63 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 486 SER cc_start: 0.8564 (m) cc_final: 0.7961 (t) REVERT: B 510 MET cc_start: 0.8738 (tpp) cc_final: 0.8480 (mmm) REVERT: B 540 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9285 (mp) outliers start: 39 outliers final: 28 residues processed: 113 average time/residue: 0.0826 time to fit residues: 15.4180 Evaluate side-chains 114 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 206 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 483 MET 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 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 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 195 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 23 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.071344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053752 restraints weight = 58246.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.055107 restraints weight = 28740.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055944 restraints weight = 18194.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.056451 restraints weight = 13477.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.056749 restraints weight = 11195.056| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12624 Z= 0.232 Angle : 0.698 10.769 17121 Z= 0.346 Chirality : 0.044 0.218 1958 Planarity : 0.004 0.044 2130 Dihedral : 5.875 75.149 1817 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.20 % Allowed : 12.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.22), residues: 1552 helix: 0.64 (0.21), residues: 646 sheet: -0.80 (0.32), residues: 274 loop : -1.15 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.018 0.002 TYR A 494 PHE 0.021 0.002 PHE D 79 TRP 0.015 0.002 TRP B 624 HIS 0.002 0.001 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00513 (12613) covalent geometry : angle 0.69476 (17095) SS BOND : bond 0.00462 ( 7) SS BOND : angle 1.09112 ( 14) hydrogen bonds : bond 0.03664 ( 486) hydrogen bonds : angle 4.86878 ( 1461) link_BETA1-4 : bond 0.00811 ( 2) link_BETA1-4 : angle 2.73837 ( 6) link_NAG-ASN : bond 0.00059 ( 2) link_NAG-ASN : angle 1.77738 ( 6) *********************** 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 119 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 76 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8280 (mmt) cc_final: 0.8023 (mmp) REVERT: A 486 SER cc_start: 0.8834 (m) cc_final: 0.8418 (t) REVERT: A 540 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9278 (mm) REVERT: B 199 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7409 (tm-30) REVERT: B 486 SER cc_start: 0.8590 (m) cc_final: 0.8207 (t) REVERT: B 510 MET cc_start: 0.8732 (tpp) cc_final: 0.8346 (tpp) REVERT: B 540 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9297 (mp) outliers start: 43 outliers final: 32 residues processed: 109 average time/residue: 0.0862 time to fit residues: 15.5599 Evaluate side-chains 109 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 195 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 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 83 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 635 CYS Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 126 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 95 optimal weight: 0.0870 chunk 61 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 40 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 = 0.3697 r_free = 0.3697 target = 0.073369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055591 restraints weight = 56845.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.057057 restraints weight = 27809.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.057959 restraints weight = 17344.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.058486 restraints weight = 12712.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058809 restraints weight = 10484.352| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.6601 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= 0.113 Angle : 0.628 10.991 17121 Z= 0.307 Chirality : 0.042 0.220 1958 Planarity : 0.003 0.043 2130 Dihedral : 5.510 75.812 1817 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.38 % Allowed : 13.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.22), residues: 1552 helix: 0.80 (0.21), residues: 650 sheet: -0.59 (0.33), residues: 270 loop : -1.06 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 383 TYR 0.009 0.001 TYR C 91 PHE 0.013 0.001 PHE D 79 TRP 0.014 0.001 TRP F 35 HIS 0.002 0.000 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00256 (12613) covalent geometry : angle 0.62569 (17095) SS BOND : bond 0.00303 ( 7) SS BOND : angle 0.90648 ( 14) hydrogen bonds : bond 0.03381 ( 486) hydrogen bonds : angle 4.61025 ( 1461) link_BETA1-4 : bond 0.00782 ( 2) link_BETA1-4 : angle 2.20702 ( 6) link_NAG-ASN : bond 0.00035 ( 2) link_NAG-ASN : angle 1.45800 ( 6) *********************** 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 121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8326 (mmt) cc_final: 0.8024 (mmp) REVERT: A 486 SER cc_start: 0.8805 (m) cc_final: 0.8440 (t) REVERT: A 540 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9249 (mp) REVERT: B 199 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7355 (tm-30) REVERT: B 421 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9293 (t) REVERT: B 486 SER cc_start: 0.8485 (m) cc_final: 0.7867 (t) REVERT: B 510 MET cc_start: 0.8789 (tpp) cc_final: 0.8458 (mmm) REVERT: B 540 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9283 (mp) REVERT: B 548 MET cc_start: 0.9355 (mtt) cc_final: 0.8871 (mtt) outliers start: 32 outliers final: 23 residues processed: 114 average time/residue: 0.0843 time to fit residues: 15.7996 Evaluate side-chains 103 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 206 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 635 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 120 optimal weight: 20.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 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 = 0.3685 r_free = 0.3685 target = 0.072293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.054433 restraints weight = 57421.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055863 restraints weight = 28481.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.056738 restraints weight = 17784.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.057237 restraints weight = 13103.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.057423 restraints weight = 10887.245| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12624 Z= 0.155 Angle : 0.664 13.034 17121 Z= 0.322 Chirality : 0.043 0.232 1958 Planarity : 0.004 0.044 2130 Dihedral : 5.488 74.108 1817 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.23 % Allowed : 14.29 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.22), residues: 1552 helix: 0.89 (0.21), residues: 646 sheet: -0.50 (0.33), residues: 270 loop : -1.10 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 39 TYR 0.011 0.001 TYR A 494 PHE 0.016 0.001 PHE D 79 TRP 0.012 0.001 TRP F 35 HIS 0.002 0.001 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00350 (12613) covalent geometry : angle 0.66190 (17095) SS BOND : bond 0.00341 ( 7) SS BOND : angle 0.87478 ( 14) hydrogen bonds : bond 0.03365 ( 486) hydrogen bonds : angle 4.66707 ( 1461) link_BETA1-4 : bond 0.00760 ( 2) link_BETA1-4 : angle 2.33126 ( 6) link_NAG-ASN : bond 0.00005 ( 2) link_NAG-ASN : angle 1.59769 ( 6) ********************** 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 110 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8343 (mmt) cc_final: 0.8016 (mmp) REVERT: A 421 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9265 (t) REVERT: A 486 SER cc_start: 0.8839 (m) cc_final: 0.8469 (t) REVERT: A 540 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9250 (mp) REVERT: B 199 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7419 (tm-30) REVERT: B 421 THR cc_start: 0.9512 (OUTLIER) cc_final: 0.9291 (t) REVERT: B 486 SER cc_start: 0.8580 (m) cc_final: 0.8186 (t) REVERT: B 510 MET cc_start: 0.8804 (tpp) cc_final: 0.8464 (tpp) REVERT: B 540 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9276 (mp) REVERT: B 548 MET cc_start: 0.9363 (mtt) cc_final: 0.8782 (mtt) outliers start: 30 outliers final: 24 residues processed: 104 average time/residue: 0.0819 time to fit residues: 14.1412 Evaluate side-chains 103 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE 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 206 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 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 83 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 540 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 131 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 0.0980 chunk 0 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN B 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.070708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.052943 restraints weight = 57634.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.054332 restraints weight = 28380.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.055212 restraints weight = 17587.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.055746 restraints weight = 12909.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056041 restraints weight = 10628.688| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.6881 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 : 0.664 11.387 17121 Z= 0.324 Chirality : 0.043 0.230 1958 Planarity : 0.004 0.044 2130 Dihedral : 5.528 71.510 1817 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.16 % Allowed : 14.43 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.22), residues: 1552 helix: 0.98 (0.21), residues: 644 sheet: -0.44 (0.33), residues: 270 loop : -1.12 (0.27), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 39 TYR 0.013 0.001 TYR A 494 PHE 0.017 0.001 PHE D 79 TRP 0.013 0.001 TRP F 35 HIS 0.002 0.001 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00391 (12613) covalent geometry : angle 0.66148 (17095) SS BOND : bond 0.00372 ( 7) SS BOND : angle 0.94926 ( 14) hydrogen bonds : bond 0.03391 ( 486) hydrogen bonds : angle 4.70252 ( 1461) link_BETA1-4 : bond 0.00805 ( 2) link_BETA1-4 : angle 2.39816 ( 6) link_NAG-ASN : bond 0.00013 ( 2) link_NAG-ASN : angle 1.63335 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2058.78 seconds wall clock time: 36 minutes 34.18 seconds (2194.18 seconds total)