Starting phenix.real_space_refine on Thu Jun 12 12:35:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yys_39677/06_2025/8yys_39677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yys_39677/06_2025/8yys_39677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yys_39677/06_2025/8yys_39677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yys_39677/06_2025/8yys_39677.map" model { file = "/net/cci-nas-00/data/ceres_data/8yys_39677/06_2025/8yys_39677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yys_39677/06_2025/8yys_39677.cif" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 108 5.16 5 C 8690 2.51 5 N 2366 2.21 5 O 2546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13710 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain breaks: 1 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain breaks: 1 Chain: "B" Number of atoms: 6492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6492 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 40, 'TRANS': 764} Chain breaks: 6 Chain: "A" Number of atoms: 6492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6492 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 40, 'TRANS': 764} Chain breaks: 6 Time building chain proxies: 9.97, per 1000 atoms: 0.73 Number of scatterers: 13710 At special positions: 0 Unit cell: (100.98, 143.22, 155.1, 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 108 16.00 O 2546 8.00 N 2366 7.00 C 8690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 41 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 41 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 215 " distance=2.03 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 228 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 243 " distance=2.03 Simple disulfide: pdb=" SG CYS B 239 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 674 " - pdb=" SG CYS B 887 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 822 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 215 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 887 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 822 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.8 seconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3204 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 34 sheets defined 16.1% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'C' and resid 9 through 19 removed outlier: 3.941A pdb=" N GLU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 14 " --> pdb=" O HIS C 10 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 removed outlier: 3.657A pdb=" N THR C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 48 removed outlier: 3.903A pdb=" N ASN C 48 " --> pdb=" O TYR C 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 19 removed outlier: 3.941A pdb=" N GLU D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 14 " --> pdb=" O HIS D 10 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 38 removed outlier: 3.658A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 48 removed outlier: 3.903A pdb=" N ASN D 48 " --> pdb=" O TYR D 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.639A pdb=" N LEU B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 405 through 409 removed outlier: 4.279A pdb=" N PHE B 408 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 462 through 472 removed outlier: 3.610A pdb=" N ILE B 466 " --> pdb=" O CYS B 462 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 476 Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 665 through 671 removed outlier: 3.852A pdb=" N LEU B 671 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 741 removed outlier: 3.726A pdb=" N LEU B 723 " --> pdb=" O ILE B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 840 removed outlier: 3.889A pdb=" N ASP B 839 " --> pdb=" O GLU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 897 removed outlier: 4.506A pdb=" N LEU B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.639A pdb=" N LEU A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 296 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.278A pdb=" N PHE A 408 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.610A pdb=" N ILE A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 665 through 671 removed outlier: 3.852A pdb=" N LEU A 671 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 741 removed outlier: 3.727A pdb=" N LEU A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.888A pdb=" N ASP A 839 " --> pdb=" O GLU A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 897 removed outlier: 4.507A pdb=" N LEU A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 40 removed outlier: 7.013A pdb=" N CYS B 35 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N HIS B 59 " --> pdb=" O CYS B 35 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY B 37 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLN B 61 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP B 39 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 40 removed outlier: 7.013A pdb=" N CYS B 35 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N HIS B 59 " --> pdb=" O CYS B 35 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY B 37 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLN B 61 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP B 39 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B 87 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 62 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 88 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N PHE B 123 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 90 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ARG B 145 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 121 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLU B 147 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE B 123 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 198 through 200 Processing sheet with id=AA4, first strand: chain 'B' and resid 209 through 211 Processing sheet with id=AA5, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AA6, first strand: chain 'B' and resid 279 through 282 removed outlier: 7.735A pdb=" N CYS B 311 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS B 274 " --> pdb=" O CYS B 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 320 through 322 Processing sheet with id=AA8, first strand: chain 'B' and resid 338 through 348 removed outlier: 10.697A pdb=" N VAL B 362 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 11.236A pdb=" N LEU B 342 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N ASN B 364 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY B 344 " --> pdb=" O ASN B 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 338 through 348 removed outlier: 10.697A pdb=" N VAL B 362 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 11.236A pdb=" N LEU B 342 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N ASN B 364 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY B 344 " --> pdb=" O ASN B 364 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 498 through 499 removed outlier: 6.845A pdb=" N GLU B 498 " --> pdb=" O LYS B 609 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AB3, first strand: chain 'B' and resid 558 through 561 Processing sheet with id=AB4, first strand: chain 'B' and resid 626 through 634 removed outlier: 5.214A pdb=" N ASP B 627 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS B 643 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 633 " --> pdb=" O GLN B 637 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLN B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 786 through 790 Processing sheet with id=AB6, first strand: chain 'B' and resid 847 through 849 Processing sheet with id=AB7, first strand: chain 'B' and resid 869 through 872 removed outlier: 5.075A pdb=" N ALA B 915 " --> pdb=" O GLY B 922 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 883 through 884 removed outlier: 3.614A pdb=" N TYR B 876 " --> pdb=" O LEU B 884 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 34 through 40 removed outlier: 7.012A pdb=" N CYS A 35 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N HIS A 59 " --> pdb=" O CYS A 35 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY A 37 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLN A 61 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 39 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 34 through 40 removed outlier: 7.012A pdb=" N CYS A 35 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N HIS A 59 " --> pdb=" O CYS A 35 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY A 37 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLN A 61 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 39 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 87 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 62 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 88 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE A 123 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 90 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ARG A 145 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 121 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLU A 147 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE A 123 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AC3, first strand: chain 'A' and resid 209 through 211 Processing sheet with id=AC4, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AC5, first strand: chain 'A' and resid 279 through 282 removed outlier: 7.735A pdb=" N CYS A 311 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS A 274 " --> pdb=" O CYS A 311 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 320 through 322 Processing sheet with id=AC7, first strand: chain 'A' and resid 338 through 348 removed outlier: 10.698A pdb=" N VAL A 362 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N LEU A 342 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N ASN A 364 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY A 344 " --> pdb=" O ASN A 364 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 338 through 348 removed outlier: 10.698A pdb=" N VAL A 362 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N LEU A 342 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N ASN A 364 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY A 344 " --> pdb=" O ASN A 364 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 498 through 499 removed outlier: 6.847A pdb=" N GLU A 498 " --> pdb=" O LYS A 609 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AD2, first strand: chain 'A' and resid 558 through 561 Processing sheet with id=AD3, first strand: chain 'A' and resid 626 through 634 removed outlier: 5.216A pdb=" N ASP A 627 " --> pdb=" O LYS A 643 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 643 " --> pdb=" O ASP A 627 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 633 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLN A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 786 through 790 Processing sheet with id=AD5, first strand: chain 'A' and resid 847 through 849 Processing sheet with id=AD6, first strand: chain 'A' and resid 869 through 872 removed outlier: 5.076A pdb=" N ALA A 915 " --> pdb=" O GLY A 922 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 883 through 884 removed outlier: 3.614A pdb=" N TYR A 876 " --> pdb=" O LEU A 884 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 840 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: 5.54 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4502 1.34 - 1.46: 3252 1.46 - 1.58: 6146 1.58 - 1.70: 0 1.70 - 1.82: 130 Bond restraints: 14030 Sorted by residual: bond pdb=" N GLY C 31 " pdb=" CA GLY C 31 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.33e+00 bond pdb=" N GLY D 31 " pdb=" CA GLY D 31 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.18e+00 bond pdb=" CA GLU B 470 " pdb=" C GLU B 470 " ideal model delta sigma weight residual 1.522 1.495 0.027 1.36e-02 5.41e+03 3.95e+00 bond pdb=" CA GLU A 470 " pdb=" C GLU A 470 " ideal model delta sigma weight residual 1.522 1.496 0.026 1.36e-02 5.41e+03 3.77e+00 bond pdb=" N ASN C 3 " pdb=" CA ASN C 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 ... (remaining 14025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 18081 1.45 - 2.91: 757 2.91 - 4.36: 142 4.36 - 5.81: 20 5.81 - 7.27: 2 Bond angle restraints: 19002 Sorted by residual: angle pdb=" N THR C 38 " pdb=" CA THR C 38 " pdb=" C THR C 38 " ideal model delta sigma weight residual 112.13 107.49 4.64 1.37e+00 5.33e-01 1.15e+01 angle pdb=" N THR D 38 " pdb=" CA THR D 38 " pdb=" C THR D 38 " ideal model delta sigma weight residual 112.13 107.49 4.64 1.37e+00 5.33e-01 1.15e+01 angle pdb=" N MET B 858 " pdb=" CA MET B 858 " pdb=" C MET B 858 " ideal model delta sigma weight residual 113.89 108.79 5.10 1.58e+00 4.01e-01 1.04e+01 angle pdb=" N MET A 858 " pdb=" CA MET A 858 " pdb=" C MET A 858 " ideal model delta sigma weight residual 113.89 108.89 5.00 1.58e+00 4.01e-01 1.00e+01 angle pdb=" N ILE A 201 " pdb=" CA ILE A 201 " pdb=" C ILE A 201 " ideal model delta sigma weight residual 111.48 108.61 2.87 9.40e-01 1.13e+00 9.32e+00 ... (remaining 18997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7525 17.74 - 35.47: 757 35.47 - 53.21: 176 53.21 - 70.95: 34 70.95 - 88.69: 16 Dihedral angle restraints: 8508 sinusoidal: 3544 harmonic: 4964 Sorted by residual: dihedral pdb=" CA ASP A 72 " pdb=" C ASP A 72 " pdb=" N PHE A 73 " pdb=" CA PHE A 73 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ASP B 72 " pdb=" C ASP B 72 " pdb=" N PHE B 73 " pdb=" CA PHE B 73 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASN A 482 " pdb=" C ASN A 482 " pdb=" N ASP A 483 " pdb=" CA ASP A 483 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 8505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1190 0.028 - 0.055: 565 0.055 - 0.083: 131 0.083 - 0.110: 128 0.110 - 0.138: 56 Chirality restraints: 2070 Sorted by residual: chirality pdb=" CA ILE B 109 " pdb=" N ILE B 109 " pdb=" C ILE B 109 " pdb=" CB ILE B 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE A 109 " pdb=" N ILE A 109 " pdb=" C ILE A 109 " pdb=" CB ILE A 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 122 " pdb=" N ILE A 122 " pdb=" C ILE A 122 " pdb=" CB ILE A 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 2067 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 822 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C CYS A 822 " -0.026 2.00e-02 2.50e+03 pdb=" O CYS A 822 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 823 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 822 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" C CYS B 822 " -0.026 2.00e-02 2.50e+03 pdb=" O CYS B 822 " 0.010 2.00e-02 2.50e+03 pdb=" N SER B 823 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 592 " 0.009 2.00e-02 2.50e+03 9.64e-03 1.63e+00 pdb=" CG PHE B 592 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 592 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 592 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 592 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 592 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 592 " 0.001 2.00e-02 2.50e+03 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 0.82 - 1.64: 4 1.64 - 2.45: 142 2.45 - 3.27: 16858 3.27 - 4.08: 37368 4.08 - 4.90: 64326 Warning: very small nonbonded interaction distances. Nonbonded interactions: 118698 Sorted by model distance: nonbonded pdb=" OD2 ASP B 601 " pdb=" NH2 ARG A 399 " model vdw 0.825 3.120 nonbonded pdb=" NH2 ARG B 399 " pdb=" OD2 ASP A 601 " model vdw 0.837 3.120 nonbonded pdb=" OD2 ASP B 601 " pdb=" CZ ARG A 399 " model vdw 1.266 3.270 nonbonded pdb=" CZ ARG B 399 " pdb=" OD2 ASP A 601 " model vdw 1.292 3.270 nonbonded pdb=" CG ASP B 601 " pdb=" NH2 ARG A 399 " model vdw 1.680 3.350 ... (remaining 118693 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: 0.07 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.510 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: 0.730 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.960 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 : 0.003 0.099 14068 Z= 0.196 Angle : 0.696 7.267 19074 Z= 0.405 Chirality : 0.043 0.138 2070 Planarity : 0.004 0.031 2454 Dihedral : 15.198 88.686 5196 Min Nonbonded Distance : 0.825 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 0.26 % Allowed : 15.74 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.19), residues: 1666 helix: -1.16 (0.38), residues: 180 sheet: -1.53 (0.29), residues: 316 loop : -2.00 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 441 HIS 0.006 0.001 HIS C 5 PHE 0.022 0.001 PHE B 592 TYR 0.020 0.002 TYR B 876 ARG 0.006 0.001 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.25548 ( 316) hydrogen bonds : angle 10.62178 ( 840) SS BOND : bond 0.00202 ( 36) SS BOND : angle 0.72385 ( 72) covalent geometry : bond 0.00308 (14030) covalent geometry : angle 0.69618 (19002) Misc. bond : bond 0.09023 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 2.076 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 MET cc_start: 0.6177 (mmm) cc_final: 0.5976 (mmm) outliers start: 4 outliers final: 0 residues processed: 106 average time/residue: 0.2810 time to fit residues: 44.4373 Evaluate side-chains 57 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 HIS D 10 HIS B 433 GLN ** A 433 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 = 0.3996 r_free = 0.3996 target = 0.082869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.057787 restraints weight = 115384.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.058229 restraints weight = 76678.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.058431 restraints weight = 57483.659| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14068 Z= 0.225 Angle : 0.795 8.308 19074 Z= 0.423 Chirality : 0.050 0.185 2070 Planarity : 0.005 0.066 2454 Dihedral : 7.150 34.914 1858 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.13 % Allowed : 5.44 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.20), residues: 1666 helix: -1.43 (0.34), residues: 194 sheet: -1.50 (0.30), residues: 278 loop : -1.80 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 859 HIS 0.034 0.003 HIS B 456 PHE 0.028 0.003 PHE B 454 TYR 0.026 0.003 TYR B 876 ARG 0.006 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.05323 ( 316) hydrogen bonds : angle 8.69812 ( 840) SS BOND : bond 0.00255 ( 36) SS BOND : angle 1.30339 ( 72) covalent geometry : bond 0.00489 (14030) covalent geometry : angle 0.79225 (19002) Misc. bond : bond 0.01370 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 1.951 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: C 15 LEU cc_start: 0.9177 (tp) cc_final: 0.8915 (tp) REVERT: D 15 LEU cc_start: 0.9168 (tp) cc_final: 0.8888 (tp) REVERT: B 65 MET cc_start: 0.6270 (mmm) cc_final: 0.6049 (mmm) REVERT: B 83 MET cc_start: 0.8283 (tmm) cc_final: 0.8014 (tmm) outliers start: 2 outliers final: 0 residues processed: 68 average time/residue: 0.3483 time to fit residues: 38.6989 Evaluate side-chains 49 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 161 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN A 340 HIS ** A 433 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 = 0.3966 r_free = 0.3966 target = 0.081481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.054635 restraints weight = 116205.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.055416 restraints weight = 78697.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.055705 restraints weight = 60881.445| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14068 Z= 0.262 Angle : 0.792 11.856 19074 Z= 0.415 Chirality : 0.050 0.197 2070 Planarity : 0.005 0.045 2454 Dihedral : 7.064 40.328 1858 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.13 % Allowed : 4.92 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.19), residues: 1666 helix: -1.86 (0.32), residues: 206 sheet: -1.37 (0.30), residues: 270 loop : -1.98 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 659 HIS 0.009 0.002 HIS B 456 PHE 0.038 0.003 PHE A 454 TYR 0.024 0.002 TYR D 16 ARG 0.006 0.001 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 316) hydrogen bonds : angle 8.47941 ( 840) SS BOND : bond 0.00425 ( 36) SS BOND : angle 1.11707 ( 72) covalent geometry : bond 0.00556 (14030) covalent geometry : angle 0.79068 (19002) Misc. bond : bond 0.00463 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 HIS cc_start: 0.8269 (m90) cc_final: 0.8029 (m170) REVERT: C 15 LEU cc_start: 0.9341 (tp) cc_final: 0.9015 (tt) REVERT: D 15 LEU cc_start: 0.9407 (tp) cc_final: 0.9199 (tt) REVERT: B 65 MET cc_start: 0.6508 (mmm) cc_final: 0.6292 (mmm) REVERT: B 596 LEU cc_start: 0.8995 (mt) cc_final: 0.8710 (mt) REVERT: A 596 LEU cc_start: 0.8984 (mt) cc_final: 0.8694 (mt) outliers start: 2 outliers final: 0 residues processed: 69 average time/residue: 0.2374 time to fit residues: 26.5124 Evaluate side-chains 46 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 167 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.089144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.060902 restraints weight = 115410.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.060224 restraints weight = 80420.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.060792 restraints weight = 56761.548| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14068 Z= 0.154 Angle : 0.705 10.134 19074 Z= 0.371 Chirality : 0.048 0.209 2070 Planarity : 0.004 0.033 2454 Dihedral : 6.681 41.303 1858 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.19), residues: 1666 helix: -1.35 (0.35), residues: 194 sheet: -1.16 (0.31), residues: 254 loop : -1.78 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 859 HIS 0.007 0.001 HIS B 847 PHE 0.025 0.002 PHE B 454 TYR 0.018 0.002 TYR C 16 ARG 0.005 0.001 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 316) hydrogen bonds : angle 8.08280 ( 840) SS BOND : bond 0.00183 ( 36) SS BOND : angle 1.32004 ( 72) covalent geometry : bond 0.00340 (14030) covalent geometry : angle 0.70148 (19002) Misc. bond : bond 0.00306 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.9335 (tp) cc_final: 0.9087 (tp) REVERT: D 15 LEU cc_start: 0.9304 (tp) cc_final: 0.9073 (tt) REVERT: B 469 MET cc_start: 0.9307 (tpp) cc_final: 0.9024 (tpp) REVERT: B 606 TYR cc_start: 0.8759 (m-10) cc_final: 0.8552 (m-10) REVERT: A 606 TYR cc_start: 0.8753 (m-10) cc_final: 0.8544 (m-10) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2476 time to fit residues: 27.9803 Evaluate side-chains 54 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 159 optimal weight: 0.0030 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 HIS ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.089577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.062064 restraints weight = 115367.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.061806 restraints weight = 79976.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.062005 restraints weight = 56900.756| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14068 Z= 0.129 Angle : 0.670 12.703 19074 Z= 0.349 Chirality : 0.047 0.219 2070 Planarity : 0.004 0.034 2454 Dihedral : 6.317 42.021 1858 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.20), residues: 1666 helix: -0.93 (0.37), residues: 184 sheet: -0.92 (0.30), residues: 282 loop : -1.59 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 659 HIS 0.015 0.001 HIS B 456 PHE 0.020 0.002 PHE B 454 TYR 0.014 0.002 TYR B 909 ARG 0.003 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 316) hydrogen bonds : angle 7.80662 ( 840) SS BOND : bond 0.00143 ( 36) SS BOND : angle 1.06251 ( 72) covalent geometry : bond 0.00283 (14030) covalent geometry : angle 0.66815 (19002) Misc. bond : bond 0.00352 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.9266 (tp) cc_final: 0.9010 (tp) REVERT: D 15 LEU cc_start: 0.9278 (tp) cc_final: 0.9052 (tt) REVERT: B 606 TYR cc_start: 0.8797 (m-10) cc_final: 0.8592 (m-10) REVERT: A 606 TYR cc_start: 0.8809 (m-10) cc_final: 0.8607 (m-10) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2370 time to fit residues: 27.4997 Evaluate side-chains 53 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 HIS ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.081489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.055441 restraints weight = 116634.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.056155 restraints weight = 76679.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.056693 restraints weight = 58238.791| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14068 Z= 0.219 Angle : 0.746 15.290 19074 Z= 0.384 Chirality : 0.048 0.228 2070 Planarity : 0.005 0.058 2454 Dihedral : 6.410 42.986 1858 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.20), residues: 1666 helix: -1.44 (0.34), residues: 208 sheet: -0.81 (0.30), residues: 292 loop : -1.82 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 659 HIS 0.011 0.002 HIS B 456 PHE 0.026 0.002 PHE A 454 TYR 0.036 0.002 TYR A 457 ARG 0.004 0.001 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 316) hydrogen bonds : angle 7.81636 ( 840) SS BOND : bond 0.00261 ( 36) SS BOND : angle 1.01441 ( 72) covalent geometry : bond 0.00469 (14030) covalent geometry : angle 0.74439 (19002) Misc. bond : bond 0.02027 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.9449 (tp) cc_final: 0.9159 (tt) REVERT: D 15 LEU cc_start: 0.9446 (tp) cc_final: 0.9184 (tt) REVERT: B 469 MET cc_start: 0.9289 (tpp) cc_final: 0.9080 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2943 time to fit residues: 30.5905 Evaluate side-chains 53 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 66 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** 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 = 0.3965 r_free = 0.3965 target = 0.081448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.055985 restraints weight = 116711.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.056018 restraints weight = 80572.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.056551 restraints weight = 60804.832| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14068 Z= 0.222 Angle : 0.763 16.642 19074 Z= 0.394 Chirality : 0.048 0.232 2070 Planarity : 0.005 0.052 2454 Dihedral : 6.464 42.728 1858 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.20), residues: 1666 helix: -1.34 (0.34), residues: 202 sheet: -0.86 (0.30), residues: 302 loop : -1.83 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 659 HIS 0.015 0.002 HIS B 226 PHE 0.025 0.002 PHE B 454 TYR 0.028 0.002 TYR A 457 ARG 0.003 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 316) hydrogen bonds : angle 7.82689 ( 840) SS BOND : bond 0.00303 ( 36) SS BOND : angle 1.70655 ( 72) covalent geometry : bond 0.00479 (14030) covalent geometry : angle 0.75677 (19002) Misc. bond : bond 0.00706 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.808 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: C 15 LEU cc_start: 0.9460 (tp) cc_final: 0.9149 (tt) REVERT: D 15 LEU cc_start: 0.9466 (tp) cc_final: 0.9192 (tt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.3045 time to fit residues: 33.5543 Evaluate side-chains 56 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 10 optimal weight: 0.0970 chunk 124 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.088564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.061516 restraints weight = 116582.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.060478 restraints weight = 82227.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.060965 restraints weight = 59420.104| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14068 Z= 0.138 Angle : 0.706 12.829 19074 Z= 0.365 Chirality : 0.048 0.270 2070 Planarity : 0.004 0.037 2454 Dihedral : 6.226 42.290 1858 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.06 % Allowed : 0.78 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.20), residues: 1666 helix: -1.01 (0.35), residues: 202 sheet: -0.80 (0.30), residues: 302 loop : -1.70 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 659 HIS 0.013 0.001 HIS B 456 PHE 0.023 0.002 PHE B 455 TYR 0.024 0.002 TYR A 457 ARG 0.009 0.001 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 316) hydrogen bonds : angle 7.64704 ( 840) SS BOND : bond 0.00191 ( 36) SS BOND : angle 1.58280 ( 72) covalent geometry : bond 0.00303 (14030) covalent geometry : angle 0.70086 (19002) Misc. bond : bond 0.00170 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 2.445 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: C 15 LEU cc_start: 0.9343 (tp) cc_final: 0.9046 (tp) REVERT: D 15 LEU cc_start: 0.9344 (tp) cc_final: 0.9082 (tp) REVERT: B 63 LEU cc_start: 0.8878 (pp) cc_final: 0.8656 (pp) REVERT: A 469 MET cc_start: 0.9162 (tpp) cc_final: 0.8949 (tpp) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.3682 time to fit residues: 42.2837 Evaluate side-chains 56 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 102 optimal weight: 0.0570 chunk 74 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 145 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.082188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.057112 restraints weight = 117136.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.057230 restraints weight = 77735.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.057667 restraints weight = 58974.471| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14068 Z= 0.131 Angle : 0.679 12.902 19074 Z= 0.355 Chirality : 0.048 0.265 2070 Planarity : 0.004 0.037 2454 Dihedral : 6.138 41.435 1858 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.99 (0.20), residues: 1666 helix: -0.84 (0.34), residues: 214 sheet: -0.75 (0.32), residues: 272 loop : -1.66 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 659 HIS 0.032 0.001 HIS A 456 PHE 0.019 0.002 PHE B 454 TYR 0.015 0.002 TYR B 519 ARG 0.005 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 316) hydrogen bonds : angle 7.55211 ( 840) SS BOND : bond 0.00172 ( 36) SS BOND : angle 1.41234 ( 72) covalent geometry : bond 0.00287 (14030) covalent geometry : angle 0.67458 (19002) Misc. bond : bond 0.00344 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 2.338 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: symmetry clash REVERT: C 15 LEU cc_start: 0.9409 (tp) cc_final: 0.9128 (tp) REVERT: D 15 LEU cc_start: 0.9359 (tp) cc_final: 0.9151 (tp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3994 time to fit residues: 49.6214 Evaluate side-chains 62 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 20.0000 chunk 162 optimal weight: 0.0170 chunk 82 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 146 optimal weight: 30.0000 chunk 147 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 overall best weight: 2.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.081189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.055350 restraints weight = 116087.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.055534 restraints weight = 81129.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.055889 restraints weight = 57941.397| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14068 Z= 0.202 Angle : 0.715 12.707 19074 Z= 0.371 Chirality : 0.048 0.206 2070 Planarity : 0.005 0.051 2454 Dihedral : 6.196 41.074 1858 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.20), residues: 1666 helix: -0.84 (0.36), residues: 202 sheet: -0.86 (0.31), residues: 292 loop : -1.72 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 659 HIS 0.009 0.002 HIS A 456 PHE 0.024 0.002 PHE B 454 TYR 0.019 0.002 TYR D 16 ARG 0.004 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 316) hydrogen bonds : angle 7.60248 ( 840) SS BOND : bond 0.00256 ( 36) SS BOND : angle 1.36507 ( 72) covalent geometry : bond 0.00440 (14030) covalent geometry : angle 0.71136 (19002) Misc. bond : bond 0.00443 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 2.787 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: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.9422 (tp) cc_final: 0.9112 (tt) REVERT: D 15 LEU cc_start: 0.9395 (tp) cc_final: 0.9183 (tt) REVERT: B 606 TYR cc_start: 0.8715 (m-10) cc_final: 0.8457 (m-80) REVERT: A 606 TYR cc_start: 0.8702 (m-10) cc_final: 0.8438 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.4159 time to fit residues: 42.9179 Evaluate side-chains 53 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 3.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 86 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN B 616 GLN ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.087468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.059773 restraints weight = 117396.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.060274 restraints weight = 78994.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.060274 restraints weight = 53304.954| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14068 Z= 0.184 Angle : 0.693 12.407 19074 Z= 0.361 Chirality : 0.047 0.217 2070 Planarity : 0.004 0.037 2454 Dihedral : 6.127 39.868 1858 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.20), residues: 1666 helix: -0.70 (0.36), residues: 200 sheet: -0.94 (0.31), residues: 292 loop : -1.74 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 659 HIS 0.017 0.002 HIS D 5 PHE 0.027 0.002 PHE A 454 TYR 0.021 0.002 TYR C 16 ARG 0.005 0.000 ARG A 74 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 316) hydrogen bonds : angle 7.53791 ( 840) SS BOND : bond 0.00242 ( 36) SS BOND : angle 1.32098 ( 72) covalent geometry : bond 0.00397 (14030) covalent geometry : angle 0.68920 (19002) Misc. bond : bond 0.00268 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6609.09 seconds wall clock time: 118 minutes 32.75 seconds (7112.75 seconds total)