Starting phenix.real_space_refine on Wed Jul 30 16:52:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nez_12295/07_2025/7nez_12295_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nez_12295/07_2025/7nez_12295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nez_12295/07_2025/7nez_12295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nez_12295/07_2025/7nez_12295.map" model { file = "/net/cci-nas-00/data/ceres_data/7nez_12295/07_2025/7nez_12295_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nez_12295/07_2025/7nez_12295_neut_trim.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.067 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 68 5.16 5 C 7965 2.51 5 N 2033 2.21 5 O 2279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12345 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: "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: "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: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'TTC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.99, per 1000 atoms: 0.73 Number of scatterers: 12345 At special positions: 0 Unit cell: (101.64, 97.02, 144.54, 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 68 16.00 O 2279 8.00 N 2033 7.00 C 7965 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=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 18 sheets defined 43.4% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.911A 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: 4.035A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.663A 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: 3.895A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.519A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 271 through 277 removed outlier: 4.147A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (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: 3.565A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.625A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 390 removed outlier: 3.582A pdb=" N SER A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.850A pdb=" N VAL A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 442 Processing helix chain 'A' and resid 444 through 451 removed outlier: 3.633A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.559A 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: 3.761A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.818A 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: 4.021A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 528 removed outlier: 3.680A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.620A pdb=" N ILE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.656A pdb=" N ILE A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.640A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.748A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.534A 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: 3.831A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.911A 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: 4.036A pdb=" N ILE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.894A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.519A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 271 through 277 removed outlier: 4.146A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (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: 3.566A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.625A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 removed outlier: 3.582A pdb=" N SER B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 413 removed outlier: 3.591A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 441 Processing helix chain 'B' and resid 443 through 451 removed outlier: 3.808A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 465 through 477 removed outlier: 3.761A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 3.818A 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: 4.021A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 527 removed outlier: 3.680A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 551 removed outlier: 3.647A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.657A pdb=" N ILE B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.640A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.748A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.534A 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: 3.832A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.590A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.882A 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: 3.591A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.882A 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 sheet with id=AA1, first strand: chain 'A' and resid 69 through 71 removed outlier: 3.571A pdb=" N GLY A 69 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS A 40 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.570A 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: 6.191A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 241 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 75 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 268 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 258 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.570A pdb=" N GLY B 69 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS B 40 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.191A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 75 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N THR B 257 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA B 77 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU B 259 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU B 79 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 268 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 258 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.654A pdb=" N TYR C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.394A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.034A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.034A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.653A pdb=" N TYR E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.394A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AB8, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.034A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.034A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1948 1.31 - 1.43: 3535 1.43 - 1.56: 7021 1.56 - 1.69: 11 1.69 - 1.82: 106 Bond restraints: 12621 Sorted by residual: bond pdb=" C16 TTC A1201 " pdb=" C17 TTC A1201 " ideal model delta sigma weight residual 1.411 1.641 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C13 TTC A1201 " pdb=" C17 TTC A1201 " ideal model delta sigma weight residual 1.359 1.571 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C15 TTC A1201 " pdb=" C16 TTC A1201 " ideal model delta sigma weight residual 1.364 1.557 -0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" C14 TTC A1201 " pdb=" C15 TTC A1201 " ideal model delta sigma weight residual 1.441 1.631 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" C13 TTC A1201 " pdb=" C9 TTC A1201 " ideal model delta sigma weight residual 1.456 1.630 -0.174 2.00e-02 2.50e+03 7.58e+01 ... (remaining 12616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 16762 2.53 - 5.06: 298 5.06 - 7.59: 37 7.59 - 10.13: 5 10.13 - 12.66: 5 Bond angle restraints: 17107 Sorted by residual: angle pdb=" N VAL B 442 " pdb=" CA VAL B 442 " pdb=" C VAL B 442 " ideal model delta sigma weight residual 112.17 100.50 11.67 9.50e-01 1.11e+00 1.51e+02 angle pdb=" N THR A 402 " pdb=" CA THR A 402 " pdb=" C THR A 402 " ideal model delta sigma weight residual 111.36 99.81 11.55 1.09e+00 8.42e-01 1.12e+02 angle pdb=" N GLY A 406 " pdb=" CA GLY A 406 " pdb=" C GLY A 406 " ideal model delta sigma weight residual 113.86 101.20 12.66 1.50e+00 4.44e-01 7.12e+01 angle pdb=" C ILE B 543 " pdb=" CA ILE B 543 " pdb=" CB ILE B 543 " ideal model delta sigma weight residual 112.14 101.79 10.35 1.35e+00 5.49e-01 5.88e+01 angle pdb=" N LEU B 430 " pdb=" CA LEU B 430 " pdb=" C LEU B 430 " ideal model delta sigma weight residual 111.07 103.60 7.47 1.07e+00 8.73e-01 4.88e+01 ... (remaining 17102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 7097 15.75 - 31.50: 309 31.50 - 47.26: 61 47.26 - 63.01: 7 63.01 - 78.76: 8 Dihedral angle restraints: 7482 sinusoidal: 2966 harmonic: 4516 Sorted by residual: dihedral pdb=" C PHE A 439 " pdb=" N PHE A 439 " pdb=" CA PHE A 439 " pdb=" CB PHE A 439 " ideal model delta harmonic sigma weight residual -122.60 -140.56 17.96 0 2.50e+00 1.60e-01 5.16e+01 dihedral pdb=" N PHE A 439 " pdb=" C PHE A 439 " pdb=" CA PHE A 439 " pdb=" CB PHE A 439 " ideal model delta harmonic sigma weight residual 122.80 137.58 -14.78 0 2.50e+00 1.60e-01 3.49e+01 dihedral pdb=" C THR A 402 " pdb=" N THR A 402 " pdb=" CA THR A 402 " pdb=" CB THR A 402 " ideal model delta harmonic sigma weight residual -122.00 -108.52 -13.48 0 2.50e+00 1.60e-01 2.91e+01 ... (remaining 7479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1913 0.152 - 0.304: 28 0.304 - 0.456: 9 0.456 - 0.607: 0 0.607 - 0.759: 1 Chirality restraints: 1951 Sorted by residual: chirality pdb=" CA PHE A 439 " pdb=" N PHE A 439 " pdb=" C PHE A 439 " pdb=" CB PHE A 439 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA GLN B 126 " pdb=" N GLN B 126 " pdb=" C GLN B 126 " pdb=" CB GLN B 126 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" C21 TTC A1201 " pdb=" C16 TTC A1201 " pdb=" C20 TTC A1201 " pdb=" O24 TTC A1201 " both_signs ideal model delta sigma weight residual False -2.50 -2.90 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 1948 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 440 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C SER B 440 " -0.067 2.00e-02 2.50e+03 pdb=" O SER B 440 " 0.025 2.00e-02 2.50e+03 pdb=" N SER B 441 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 437 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C GLN A 437 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN A 437 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS A 438 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 125 " -0.016 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C VAL B 125 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL B 125 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN B 126 " -0.017 2.00e-02 2.50e+03 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 97 2.55 - 3.13: 10101 3.13 - 3.72: 18747 3.72 - 4.31: 27089 4.31 - 4.90: 44567 Nonbonded interactions: 100601 Sorted by model distance: nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 1.958 3.040 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 1.958 3.040 nonbonded pdb=" OH TYR C 36 " pdb=" OE1 GLN C 89 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR E 36 " pdb=" OE1 GLN E 89 " model vdw 2.183 3.040 nonbonded pdb=" O ILE C 2 " pdb=" OG1 THR C 97 " model vdw 2.183 3.040 ... (remaining 100596 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 or resid 1202)) selection = (chain 'B' and (resid 35 through 654 or resid 702)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'D' and resid 2 through 119) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.590 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 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 0.230 12628 Z= 0.544 Angle : 0.798 12.658 17121 Z= 0.499 Chirality : 0.059 0.759 1951 Planarity : 0.004 0.038 2130 Dihedral : 9.749 78.761 4577 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.67 % Allowed : 3.79 % Favored : 95.54 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.20), residues: 1552 helix: -1.06 (0.19), residues: 602 sheet: -1.96 (0.30), residues: 252 loop : -1.92 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 627 HIS 0.004 0.001 HIS B 457 PHE 0.021 0.002 PHE B 545 TYR 0.013 0.001 TYR F 95 ARG 0.002 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.18223 ( 498) hydrogen bonds : angle 7.89009 ( 1494) SS BOND : bond 0.00221 ( 7) SS BOND : angle 2.24724 ( 14) covalent geometry : bond 0.00889 (12621) covalent geometry : angle 0.79619 (17107) *********************** 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 393 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 384 time to evaluate : 1.483 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: symmetry clash REVERT: A 168 LEU cc_start: 0.8216 (mt) cc_final: 0.8014 (tp) REVERT: A 186 VAL cc_start: 0.5535 (t) cc_final: 0.4964 (p) REVERT: A 198 MET cc_start: 0.6399 (mtp) cc_final: 0.6189 (mtp) REVERT: A 264 LEU cc_start: 0.5610 (tp) cc_final: 0.5375 (tp) REVERT: A 446 GLU cc_start: 0.8823 (tt0) cc_final: 0.8373 (tm-30) REVERT: A 450 VAL cc_start: 0.8924 (t) cc_final: 0.8504 (m) REVERT: A 475 LEU cc_start: 0.8404 (tp) cc_final: 0.8156 (mp) REVERT: A 491 CYS cc_start: 0.7666 (m) cc_final: 0.7280 (m) REVERT: A 509 MET cc_start: 0.7875 (ttt) cc_final: 0.7558 (ttp) REVERT: A 534 VAL cc_start: 0.8622 (t) cc_final: 0.8353 (m) REVERT: A 544 CYS cc_start: 0.9028 (m) cc_final: 0.8582 (m) REVERT: B 152 MET cc_start: -0.0101 (mtp) cc_final: -0.0373 (mmp) REVERT: B 198 MET cc_start: 0.6646 (mtp) cc_final: 0.6350 (mmt) REVERT: B 227 LEU cc_start: 0.6829 (tp) cc_final: 0.6304 (tp) REVERT: B 255 SER cc_start: 0.7377 (t) cc_final: 0.6610 (t) REVERT: B 288 ASN cc_start: 0.7414 (t0) cc_final: 0.6930 (p0) REVERT: B 523 MET cc_start: 0.8768 (ttt) cc_final: 0.8416 (ttm) REVERT: B 540 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8651 (mp) REVERT: B 544 CYS cc_start: 0.9257 (m) cc_final: 0.8943 (m) REVERT: B 584 ASN cc_start: 0.7631 (t0) cc_final: 0.7421 (t0) REVERT: C 17 ASP cc_start: 0.7552 (t70) cc_final: 0.7149 (t0) REVERT: D 6 GLU cc_start: 0.8112 (mp0) cc_final: 0.7890 (mp0) REVERT: D 44 LYS cc_start: 0.7895 (mptp) cc_final: 0.7610 (mmtm) REVERT: E 17 ASP cc_start: 0.6756 (t70) cc_final: 0.5919 (m-30) REVERT: E 33 LEU cc_start: 0.8864 (tm) cc_final: 0.8631 (tm) REVERT: E 79 GLN cc_start: 0.8234 (mm110) cc_final: 0.8017 (mm-40) REVERT: F 100 TYR cc_start: 0.7193 (t80) cc_final: 0.6868 (t80) outliers start: 9 outliers final: 3 residues processed: 391 average time/residue: 0.2705 time to fit residues: 149.2265 Evaluate side-chains 236 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 540 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 116 ASN A 120 ASN A 243 HIS A 375 HIS ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN B 109 ASN B 243 HIS B 582 GLN B 617 GLN D 5 GLN D 78 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.154526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.124715 restraints weight = 23995.581| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.92 r_work: 0.3656 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12628 Z= 0.140 Angle : 0.657 7.969 17121 Z= 0.335 Chirality : 0.044 0.218 1951 Planarity : 0.004 0.040 2130 Dihedral : 7.123 63.597 1806 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.98 % Allowed : 10.57 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.21), residues: 1552 helix: -0.28 (0.19), residues: 640 sheet: -1.62 (0.30), residues: 262 loop : -1.77 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 379 HIS 0.006 0.001 HIS A 457 PHE 0.023 0.002 PHE A 250 TYR 0.025 0.002 TYR E 91 ARG 0.009 0.001 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 498) hydrogen bonds : angle 5.20030 ( 1494) SS BOND : bond 0.00422 ( 7) SS BOND : angle 0.95341 ( 14) covalent geometry : bond 0.00304 (12621) covalent geometry : angle 0.65633 (17107) *********************** 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 299 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.5104 (t-90) cc_final: 0.4827 (t-170) REVERT: A 193 ARG cc_start: 0.7288 (mtt180) cc_final: 0.7054 (mtp85) REVERT: A 198 MET cc_start: 0.6907 (mtp) cc_final: 0.6591 (mtm) REVERT: A 211 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6648 (pp20) REVERT: A 451 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7478 (tp30) REVERT: A 475 LEU cc_start: 0.8823 (tp) cc_final: 0.8462 (mp) REVERT: A 483 MET cc_start: 0.7026 (ptt) cc_final: 0.6658 (ppp) REVERT: A 491 CYS cc_start: 0.8163 (m) cc_final: 0.7799 (m) REVERT: A 509 MET cc_start: 0.8211 (ttt) cc_final: 0.7953 (ttt) REVERT: A 581 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8876 (mp) REVERT: B 71 MET cc_start: 0.5346 (mmp) cc_final: 0.4491 (mmm) REVERT: B 152 MET cc_start: 0.0423 (mtp) cc_final: 0.0027 (mmp) REVERT: B 162 ASN cc_start: 0.8762 (t0) cc_final: 0.8236 (m-40) REVERT: B 198 MET cc_start: 0.7361 (mtp) cc_final: 0.6695 (mmt) REVERT: B 227 LEU cc_start: 0.6747 (tp) cc_final: 0.6282 (mp) REVERT: B 231 MET cc_start: 0.8822 (mtt) cc_final: 0.8417 (ptp) REVERT: B 288 ASN cc_start: 0.7656 (t0) cc_final: 0.7088 (p0) REVERT: B 442 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8972 (p) REVERT: B 536 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8430 (p) REVERT: B 540 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8327 (mt) REVERT: B 544 CYS cc_start: 0.9177 (m) cc_final: 0.8865 (m) REVERT: B 620 ASP cc_start: 0.8099 (t0) cc_final: 0.7831 (t0) REVERT: C 17 ASP cc_start: 0.7695 (t70) cc_final: 0.7417 (t0) REVERT: E 17 ASP cc_start: 0.7268 (t70) cc_final: 0.6466 (m-30) REVERT: E 79 GLN cc_start: 0.8283 (mm110) cc_final: 0.7573 (mp10) outliers start: 40 outliers final: 17 residues processed: 281 average time/residue: 0.2546 time to fit residues: 104.8656 Evaluate side-chains 223 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain F residue 25 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 144 optimal weight: 0.0020 chunk 111 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 120 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN B 457 HIS ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 601 ASN D 5 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.141110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110978 restraints weight = 24287.756| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.95 r_work: 0.3455 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12628 Z= 0.238 Angle : 0.750 11.373 17121 Z= 0.384 Chirality : 0.046 0.210 1951 Planarity : 0.005 0.042 2130 Dihedral : 7.271 65.880 1801 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.65 % Allowed : 13.62 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.21), residues: 1552 helix: 0.05 (0.20), residues: 650 sheet: -1.29 (0.31), residues: 272 loop : -1.73 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 379 HIS 0.011 0.002 HIS A 457 PHE 0.034 0.002 PHE B 385 TYR 0.022 0.002 TYR F 95 ARG 0.013 0.001 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 498) hydrogen bonds : angle 5.02651 ( 1494) SS BOND : bond 0.00686 ( 7) SS BOND : angle 1.42921 ( 14) covalent geometry : bond 0.00523 (12621) covalent geometry : angle 0.74910 (17107) *********************** 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 285 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 4.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.6130 (mtt) cc_final: 0.5911 (mmt) REVERT: A 90 LEU cc_start: 0.4482 (OUTLIER) cc_final: 0.3233 (mt) REVERT: A 198 MET cc_start: 0.6983 (mtp) cc_final: 0.6662 (mtm) REVERT: A 239 ILE cc_start: 0.7483 (mt) cc_final: 0.7262 (mm) REVERT: A 407 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8843 (mp) REVERT: A 451 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7845 (tp30) REVERT: A 483 MET cc_start: 0.7341 (ptt) cc_final: 0.7093 (ppp) REVERT: A 491 CYS cc_start: 0.8895 (m) cc_final: 0.8526 (m) REVERT: B 162 ASN cc_start: 0.8884 (t0) cc_final: 0.8496 (m-40) REVERT: B 288 ASN cc_start: 0.7743 (t0) cc_final: 0.6973 (p0) REVERT: B 451 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8673 (mt-10) REVERT: B 540 LEU cc_start: 0.8975 (mm) cc_final: 0.8479 (mt) REVERT: C 82 ASP cc_start: 0.8334 (m-30) cc_final: 0.8063 (t0) REVERT: D 5 GLN cc_start: 0.7811 (mm110) cc_final: 0.7380 (mm-40) REVERT: E 11 PHE cc_start: 0.8422 (m-80) cc_final: 0.8189 (m-80) REVERT: F 20 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7619 (mt) outliers start: 49 outliers final: 26 residues processed: 264 average time/residue: 0.3706 time to fit residues: 145.8557 Evaluate side-chains 216 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 49 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 80 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 143 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS A 583 HIS A 584 ASN B 109 ASN ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.139501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.110650 restraints weight = 24191.516| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.76 r_work: 0.3479 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12628 Z= 0.279 Angle : 0.766 10.532 17121 Z= 0.387 Chirality : 0.048 0.294 1951 Planarity : 0.005 0.044 2130 Dihedral : 7.118 65.078 1797 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.61 % Allowed : 15.10 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1552 helix: 0.07 (0.20), residues: 648 sheet: -1.07 (0.32), residues: 272 loop : -1.81 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 379 HIS 0.008 0.002 HIS A 457 PHE 0.028 0.002 PHE F 79 TYR 0.019 0.002 TYR B 123 ARG 0.007 0.001 ARG B 383 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 498) hydrogen bonds : angle 5.06227 ( 1494) SS BOND : bond 0.01186 ( 7) SS BOND : angle 1.99924 ( 14) covalent geometry : bond 0.00632 (12621) covalent geometry : angle 0.76384 (17107) *********************** 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 278 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 216 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.5320 (OUTLIER) cc_final: 0.4166 (tp) REVERT: A 451 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7958 (tp30) REVERT: A 491 CYS cc_start: 0.8954 (m) cc_final: 0.8575 (m) REVERT: B 211 GLU cc_start: 0.7602 (pt0) cc_final: 0.7096 (pt0) REVERT: B 247 TYR cc_start: 0.5578 (t80) cc_final: 0.5303 (t80) REVERT: B 288 ASN cc_start: 0.7692 (t0) cc_final: 0.6716 (p0) REVERT: B 451 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8532 (mt-10) REVERT: C 18 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8388 (ttp80) REVERT: F 20 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7511 (mt) outliers start: 62 outliers final: 42 residues processed: 258 average time/residue: 0.2861 time to fit residues: 111.9862 Evaluate side-chains 237 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 49 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 134 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 104 optimal weight: 0.0770 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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** B 583 HIS D 5 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.135446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.105160 restraints weight = 24152.163| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.01 r_work: 0.3341 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12628 Z= 0.177 Angle : 0.656 14.261 17121 Z= 0.329 Chirality : 0.044 0.236 1951 Planarity : 0.004 0.044 2130 Dihedral : 6.857 65.773 1797 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.65 % Allowed : 17.93 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1552 helix: 0.32 (0.20), residues: 648 sheet: -0.95 (0.32), residues: 272 loop : -1.66 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 379 HIS 0.004 0.001 HIS A 350 PHE 0.028 0.002 PHE B 506 TYR 0.016 0.002 TYR B 44 ARG 0.004 0.001 ARG B 383 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 498) hydrogen bonds : angle 4.76908 ( 1494) SS BOND : bond 0.00523 ( 7) SS BOND : angle 1.19841 ( 14) covalent geometry : bond 0.00410 (12621) covalent geometry : angle 0.65580 (17107) *********************** 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 256 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.4234 (tp) REVERT: A 131 MET cc_start: 0.6986 (mmm) cc_final: 0.6367 (mtp) REVERT: A 193 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7687 (mtt-85) REVERT: A 198 MET cc_start: 0.6984 (mtp) cc_final: 0.6703 (mtp) REVERT: A 407 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8756 (mp) REVERT: A 451 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7714 (tp30) REVERT: A 491 CYS cc_start: 0.8910 (m) cc_final: 0.8528 (m) REVERT: B 247 TYR cc_start: 0.5555 (t80) cc_final: 0.5300 (t80) REVERT: B 288 ASN cc_start: 0.7526 (t0) cc_final: 0.6498 (p0) REVERT: B 451 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8629 (mt-10) REVERT: C 18 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8364 (ttp80) REVERT: C 82 ASP cc_start: 0.8294 (m-30) cc_final: 0.7907 (t0) REVERT: F 20 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7405 (mt) outliers start: 49 outliers final: 41 residues processed: 240 average time/residue: 0.2267 time to fit residues: 82.4011 Evaluate side-chains 231 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 49 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.138219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.108018 restraints weight = 24102.461| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.04 r_work: 0.3398 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 12628 Z= 0.111 Angle : 0.609 9.937 17121 Z= 0.302 Chirality : 0.042 0.225 1951 Planarity : 0.003 0.043 2130 Dihedral : 6.556 66.229 1797 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.57 % Allowed : 18.45 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1552 helix: 0.58 (0.21), residues: 648 sheet: -0.76 (0.32), residues: 272 loop : -1.55 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 379 HIS 0.011 0.001 HIS A 40 PHE 0.029 0.001 PHE B 506 TYR 0.018 0.001 TYR D 51 ARG 0.004 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 498) hydrogen bonds : angle 4.43375 ( 1494) SS BOND : bond 0.00167 ( 7) SS BOND : angle 0.77709 ( 14) covalent geometry : bond 0.00247 (12621) covalent geometry : angle 0.60934 (17107) *********************** 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 262 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4339 (tp) REVERT: A 131 MET cc_start: 0.6929 (mmm) cc_final: 0.6382 (mtp) REVERT: A 193 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7655 (mtt-85) REVERT: A 231 MET cc_start: 0.8714 (mmm) cc_final: 0.8474 (mtp) REVERT: A 451 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7657 (tp30) REVERT: A 483 MET cc_start: 0.7259 (ptt) cc_final: 0.6967 (ppp) REVERT: A 491 CYS cc_start: 0.8847 (m) cc_final: 0.8453 (m) REVERT: B 198 MET cc_start: 0.8425 (ttp) cc_final: 0.8103 (ttt) REVERT: B 247 TYR cc_start: 0.5580 (t80) cc_final: 0.5318 (t80) REVERT: B 283 HIS cc_start: 0.3762 (t-90) cc_final: 0.3189 (m-70) REVERT: B 451 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8607 (mt-10) REVERT: C 82 ASP cc_start: 0.8167 (m-30) cc_final: 0.7849 (t0) REVERT: F 20 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7333 (mt) outliers start: 48 outliers final: 31 residues processed: 245 average time/residue: 0.2085 time to fit residues: 77.3669 Evaluate side-chains 226 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.135489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.106406 restraints weight = 24186.788| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.93 r_work: 0.3392 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12628 Z= 0.202 Angle : 0.688 15.140 17121 Z= 0.344 Chirality : 0.044 0.234 1951 Planarity : 0.004 0.045 2130 Dihedral : 6.676 65.652 1797 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.65 % Allowed : 18.53 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1552 helix: 0.59 (0.21), residues: 648 sheet: -0.77 (0.32), residues: 272 loop : -1.53 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 379 HIS 0.005 0.001 HIS A 40 PHE 0.028 0.002 PHE B 506 TYR 0.023 0.002 TYR B 518 ARG 0.005 0.001 ARG B 230 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 498) hydrogen bonds : angle 4.63400 ( 1494) SS BOND : bond 0.00500 ( 7) SS BOND : angle 1.83191 ( 14) covalent geometry : bond 0.00468 (12621) covalent geometry : angle 0.68651 (17107) *********************** 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 248 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.7069 (mmm) cc_final: 0.6460 (mmm) REVERT: A 193 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7634 (mtt-85) REVERT: A 451 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7771 (tp30) REVERT: A 483 MET cc_start: 0.7334 (ptt) cc_final: 0.7022 (ppp) REVERT: A 491 CYS cc_start: 0.8840 (m) cc_final: 0.8487 (m) REVERT: A 510 MET cc_start: 0.8850 (ttp) cc_final: 0.8579 (ttm) REVERT: B 198 MET cc_start: 0.8420 (ttp) cc_final: 0.8059 (ttt) REVERT: B 247 TYR cc_start: 0.5916 (t80) cc_final: 0.5621 (t80) REVERT: B 283 HIS cc_start: 0.3631 (t-90) cc_final: 0.2909 (m-70) REVERT: B 451 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8656 (mt-10) REVERT: B 636 MET cc_start: 0.8650 (mtm) cc_final: 0.8429 (mtp) REVERT: C 82 ASP cc_start: 0.8182 (m-30) cc_final: 0.7864 (t0) REVERT: F 20 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7493 (mt) outliers start: 49 outliers final: 39 residues processed: 237 average time/residue: 0.2185 time to fit residues: 79.3223 Evaluate side-chains 229 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 17 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN A 76 ASN A 234 GLN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.134598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105219 restraints weight = 24238.571| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.85 r_work: 0.3405 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12628 Z= 0.162 Angle : 0.669 17.454 17121 Z= 0.329 Chirality : 0.043 0.273 1951 Planarity : 0.004 0.044 2130 Dihedral : 6.604 66.328 1797 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.98 % Allowed : 19.72 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1552 helix: 0.68 (0.21), residues: 650 sheet: -0.76 (0.32), residues: 272 loop : -1.43 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 379 HIS 0.006 0.001 HIS A 40 PHE 0.030 0.002 PHE B 506 TYR 0.016 0.001 TYR D 51 ARG 0.004 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 498) hydrogen bonds : angle 4.53612 ( 1494) SS BOND : bond 0.00311 ( 7) SS BOND : angle 1.27073 ( 14) covalent geometry : bond 0.00374 (12621) covalent geometry : angle 0.66849 (17107) *********************** 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 236 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6979 (mmm) cc_final: 0.6546 (mmm) REVERT: A 193 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7584 (mtt-85) REVERT: A 451 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7697 (tp30) REVERT: A 483 MET cc_start: 0.7310 (ptt) cc_final: 0.7013 (ppp) REVERT: A 491 CYS cc_start: 0.8835 (m) cc_final: 0.8473 (m) REVERT: A 510 MET cc_start: 0.8789 (ttp) cc_final: 0.8517 (ttm) REVERT: B 198 MET cc_start: 0.8422 (ttp) cc_final: 0.7817 (tpp) REVERT: B 247 TYR cc_start: 0.5892 (t80) cc_final: 0.5610 (t80) REVERT: B 283 HIS cc_start: 0.3557 (t-90) cc_final: 0.2861 (m-70) REVERT: B 636 MET cc_start: 0.8639 (mtm) cc_final: 0.8433 (mtp) REVERT: C 82 ASP cc_start: 0.8137 (m-30) cc_final: 0.7837 (t0) REVERT: F 20 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7454 (mt) outliers start: 40 outliers final: 34 residues processed: 227 average time/residue: 0.2298 time to fit residues: 77.2168 Evaluate side-chains 223 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 10 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.138029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.109074 restraints weight = 24153.090| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.92 r_work: 0.3434 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12628 Z= 0.115 Angle : 0.648 15.165 17121 Z= 0.318 Chirality : 0.042 0.217 1951 Planarity : 0.003 0.043 2130 Dihedral : 6.396 64.841 1797 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.53 % Allowed : 20.39 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1552 helix: 0.91 (0.21), residues: 630 sheet: -0.68 (0.32), residues: 272 loop : -1.27 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 379 HIS 0.006 0.001 HIS A 40 PHE 0.032 0.001 PHE A 506 TYR 0.023 0.001 TYR B 518 ARG 0.005 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 498) hydrogen bonds : angle 4.33272 ( 1494) SS BOND : bond 0.00191 ( 7) SS BOND : angle 1.23001 ( 14) covalent geometry : bond 0.00259 (12621) covalent geometry : angle 0.64704 (17107) *********************** 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 228 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.5434 (OUTLIER) cc_final: 0.5185 (mt) REVERT: A 131 MET cc_start: 0.6950 (mmm) cc_final: 0.6549 (mtp) REVERT: A 193 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7643 (mtt-85) REVERT: A 451 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7575 (tp30) REVERT: A 483 MET cc_start: 0.7216 (ptt) cc_final: 0.6944 (ppp) REVERT: A 510 MET cc_start: 0.8684 (ttp) cc_final: 0.8414 (ttm) REVERT: B 198 MET cc_start: 0.8394 (ttp) cc_final: 0.7397 (tpp) REVERT: B 247 TYR cc_start: 0.5902 (t80) cc_final: 0.5638 (t80) REVERT: B 283 HIS cc_start: 0.3629 (t-90) cc_final: 0.2983 (m-70) REVERT: C 82 ASP cc_start: 0.8102 (m-30) cc_final: 0.7834 (t0) REVERT: F 20 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7364 (mt) outliers start: 34 outliers final: 29 residues processed: 219 average time/residue: 0.2189 time to fit residues: 72.0562 Evaluate side-chains 220 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 25 optimal weight: 0.0970 chunk 41 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3949 r_free = 0.3949 target = 0.137403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108827 restraints weight = 23916.784| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.89 r_work: 0.3444 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.7385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12628 Z= 0.125 Angle : 0.654 14.790 17121 Z= 0.320 Chirality : 0.042 0.216 1951 Planarity : 0.003 0.043 2130 Dihedral : 6.284 65.202 1797 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.83 % Allowed : 20.54 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1552 helix: 0.89 (0.21), residues: 644 sheet: -0.74 (0.31), residues: 292 loop : -1.17 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 379 HIS 0.006 0.001 HIS A 40 PHE 0.029 0.001 PHE B 506 TYR 0.018 0.001 TYR D 51 ARG 0.004 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 498) hydrogen bonds : angle 4.33481 ( 1494) SS BOND : bond 0.00229 ( 7) SS BOND : angle 1.18282 ( 14) covalent geometry : bond 0.00287 (12621) covalent geometry : angle 0.65305 (17107) ********************** 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 230 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6942 (mmm) cc_final: 0.6546 (mmm) REVERT: A 193 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7604 (mtt-85) REVERT: A 451 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7624 (tp30) REVERT: A 483 MET cc_start: 0.7215 (ptt) cc_final: 0.6943 (ppp) REVERT: A 510 MET cc_start: 0.8687 (ttp) cc_final: 0.8435 (ttm) REVERT: B 152 MET cc_start: 0.1071 (mtm) cc_final: 0.0850 (mpp) REVERT: B 198 MET cc_start: 0.8400 (ttp) cc_final: 0.7473 (tpp) REVERT: B 247 TYR cc_start: 0.6014 (t80) cc_final: 0.5740 (t80) REVERT: B 283 HIS cc_start: 0.3565 (t-90) cc_final: 0.2907 (m-70) REVERT: B 451 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8531 (mt-10) REVERT: C 82 ASP cc_start: 0.8053 (m-30) cc_final: 0.7800 (t0) REVERT: F 20 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7451 (mt) outliers start: 38 outliers final: 32 residues processed: 219 average time/residue: 0.2151 time to fit residues: 71.1891 Evaluate side-chains 219 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 5 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 123 optimal weight: 0.0670 chunk 127 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 557 ASN A 584 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.139046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.110418 restraints weight = 24081.156| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.91 r_work: 0.3466 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.7504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12628 Z= 0.110 Angle : 0.640 16.001 17121 Z= 0.311 Chirality : 0.041 0.204 1951 Planarity : 0.003 0.043 2130 Dihedral : 6.102 63.940 1797 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.16 % Allowed : 21.43 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1552 helix: 0.98 (0.21), residues: 634 sheet: -0.71 (0.31), residues: 290 loop : -0.97 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 379 HIS 0.006 0.001 HIS A 40 PHE 0.029 0.001 PHE B 506 TYR 0.020 0.001 TYR D 51 ARG 0.006 0.000 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 498) hydrogen bonds : angle 4.21134 ( 1494) SS BOND : bond 0.00204 ( 7) SS BOND : angle 1.05795 ( 14) covalent geometry : bond 0.00249 (12621) covalent geometry : angle 0.63928 (17107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6006.57 seconds wall clock time: 107 minutes 50.85 seconds (6470.85 seconds total)