Starting phenix.real_space_refine on Thu Sep 18 04:12:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yys_39677/09_2025/8yys_39677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yys_39677/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yys_39677/09_2025/8yys_39677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yys_39677/09_2025/8yys_39677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yys_39677/09_2025/8yys_39677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yys_39677/09_2025/8yys_39677.map" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.28, per 1000 atoms: 0.24 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: 1.04 Conformation dependent library (CDL) restraints added in 601.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.62 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: 2.75 Time building geometry restraints manager: 1.43 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'A' } 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: 13.490 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.930 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.470 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (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 ARG 0.006 0.001 ARG A 398 TYR 0.020 0.002 TYR B 876 PHE 0.022 0.001 PHE B 592 TRP 0.017 0.002 TRP B 441 HIS 0.006 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00308 (14030) covalent geometry : angle 0.69618 (19002) SS BOND : bond 0.00202 ( 36) SS BOND : angle 0.72385 ( 72) hydrogen bonds : bond 0.25548 ( 316) hydrogen bonds : angle 10.62178 ( 840) 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 : 0.605 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: 0.1258 time to fit residues: 19.8444 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 : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** 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 = 0.4041 r_free = 0.4041 target = 0.091053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.063457 restraints weight = 113310.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.062848 restraints weight = 79317.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.063378 restraints weight = 57224.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.063707 restraints weight = 44787.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.063815 restraints weight = 38275.555| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14068 Z= 0.160 Angle : 0.769 8.335 19074 Z= 0.408 Chirality : 0.050 0.198 2070 Planarity : 0.005 0.049 2454 Dihedral : 6.907 33.403 1858 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.13 % Allowed : 4.02 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.20), residues: 1666 helix: -0.79 (0.36), residues: 194 sheet: -1.44 (0.30), residues: 282 loop : -1.69 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 744 TYR 0.026 0.002 TYR B 876 PHE 0.024 0.002 PHE B 454 TRP 0.032 0.002 TRP B 859 HIS 0.018 0.002 HIS B 847 Details of bonding type rmsd covalent geometry : bond 0.00336 (14030) covalent geometry : angle 0.76686 (19002) SS BOND : bond 0.00331 ( 36) SS BOND : angle 1.27246 ( 72) hydrogen bonds : bond 0.05032 ( 316) hydrogen bonds : angle 8.43130 ( 840) Misc. bond : bond 0.01197 ( 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 89 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.528 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: C 15 LEU cc_start: 0.9009 (tp) cc_final: 0.8738 (tp) REVERT: D 15 LEU cc_start: 0.8983 (tp) cc_final: 0.8714 (tp) outliers start: 2 outliers final: 0 residues processed: 87 average time/residue: 0.1015 time to fit residues: 13.8630 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 : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 81 optimal weight: 0.3980 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.089502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.061505 restraints weight = 113842.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.060655 restraints weight = 81497.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.061105 restraints weight = 57433.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.061283 restraints weight = 45542.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.061410 restraints weight = 39263.448| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14068 Z= 0.164 Angle : 0.698 11.134 19074 Z= 0.369 Chirality : 0.048 0.217 2070 Planarity : 0.004 0.036 2454 Dihedral : 6.572 36.394 1858 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.20), residues: 1666 helix: -1.26 (0.34), residues: 206 sheet: -0.98 (0.32), residues: 248 loop : -1.71 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.020 0.002 TYR C 16 PHE 0.033 0.002 PHE B 454 TRP 0.012 0.001 TRP A 859 HIS 0.014 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00361 (14030) covalent geometry : angle 0.69683 (19002) SS BOND : bond 0.00218 ( 36) SS BOND : angle 1.03194 ( 72) hydrogen bonds : bond 0.04428 ( 316) hydrogen bonds : angle 8.06520 ( 840) Misc. bond : bond 0.00444 ( 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 78 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.523 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 10 HIS cc_start: 0.8264 (m-70) cc_final: 0.8043 (m170) REVERT: C 15 LEU cc_start: 0.9242 (tp) cc_final: 0.9038 (tp) REVERT: D 10 HIS cc_start: 0.8294 (m-70) cc_final: 0.8067 (m170) REVERT: D 15 LEU cc_start: 0.9248 (tp) cc_final: 0.9046 (tp) REVERT: B 596 LEU cc_start: 0.9005 (mt) cc_final: 0.8770 (mt) REVERT: A 596 LEU cc_start: 0.8988 (mt) cc_final: 0.8749 (mt) outliers start: 2 outliers final: 0 residues processed: 76 average time/residue: 0.0979 time to fit residues: 11.8400 Evaluate side-chains 55 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 41 optimal weight: 0.8980 chunk 52 optimal weight: 0.0010 chunk 164 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 143 optimal weight: 30.0000 chunk 17 optimal weight: 0.2980 chunk 111 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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 856 HIS A 340 HIS ** A 432 ASN ** 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 = 0.4041 r_free = 0.4041 target = 0.084243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.057867 restraints weight = 116092.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.058399 restraints weight = 73701.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.058846 restraints weight = 55062.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.059128 restraints weight = 45835.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.059361 restraints weight = 40903.565| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14068 Z= 0.127 Angle : 0.666 10.437 19074 Z= 0.350 Chirality : 0.047 0.217 2070 Planarity : 0.004 0.036 2454 Dihedral : 6.298 37.096 1858 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.20), residues: 1666 helix: -1.02 (0.35), residues: 206 sheet: -1.09 (0.31), residues: 252 loop : -1.59 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.016 0.002 TYR A 909 PHE 0.019 0.002 PHE B 454 TRP 0.010 0.001 TRP B 659 HIS 0.017 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00278 (14030) covalent geometry : angle 0.66196 (19002) SS BOND : bond 0.00206 ( 36) SS BOND : angle 1.42140 ( 72) hydrogen bonds : bond 0.03884 ( 316) hydrogen bonds : angle 7.73190 ( 840) Misc. bond : bond 0.00620 ( 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 79 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.589 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: 0.9161 (tp) cc_final: 0.8943 (tp) REVERT: D 15 LEU cc_start: 0.9159 (tp) cc_final: 0.8949 (tp) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0989 time to fit residues: 12.8803 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 : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 150 optimal weight: 40.0000 chunk 30 optimal weight: 0.4980 chunk 126 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 ASN A 364 ASN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** 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 = 0.4007 r_free = 0.4007 target = 0.082918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.056596 restraints weight = 115930.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057278 restraints weight = 76476.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.057870 restraints weight = 56666.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.058124 restraints weight = 47577.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.058042 restraints weight = 41988.310| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14068 Z= 0.158 Angle : 0.670 12.264 19074 Z= 0.349 Chirality : 0.046 0.219 2070 Planarity : 0.004 0.036 2454 Dihedral : 6.138 38.219 1858 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.20), residues: 1666 helix: -1.13 (0.34), residues: 212 sheet: -0.84 (0.32), residues: 244 loop : -1.64 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 145 TYR 0.019 0.002 TYR D 26 PHE 0.023 0.002 PHE B 454 TRP 0.009 0.001 TRP B 659 HIS 0.011 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00345 (14030) covalent geometry : angle 0.66777 (19002) SS BOND : bond 0.00185 ( 36) SS BOND : angle 1.08358 ( 72) hydrogen bonds : bond 0.03821 ( 316) hydrogen bonds : angle 7.51560 ( 840) Misc. bond : bond 0.00463 ( 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 65 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.9333 (tp) cc_final: 0.9076 (tp) REVERT: D 15 LEU cc_start: 0.9332 (tp) cc_final: 0.9089 (tp) REVERT: A 430 LEU cc_start: 0.9035 (tt) cc_final: 0.8824 (tt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0979 time to fit residues: 10.3175 Evaluate side-chains 52 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 165 optimal weight: 20.0000 chunk 116 optimal weight: 0.0170 chunk 163 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 overall best weight: 3.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 ASN A 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.088294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.060661 restraints weight = 118537.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.059466 restraints weight = 84541.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.059865 restraints weight = 60024.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.060227 restraints weight = 48205.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.060201 restraints weight = 40921.764| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 14068 Z= 0.221 Angle : 0.726 14.642 19074 Z= 0.377 Chirality : 0.048 0.272 2070 Planarity : 0.005 0.048 2454 Dihedral : 6.287 39.554 1858 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.20), residues: 1666 helix: -1.23 (0.34), residues: 212 sheet: -0.74 (0.31), residues: 272 loop : -1.70 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 110 TYR 0.023 0.002 TYR A 87 PHE 0.027 0.002 PHE B 454 TRP 0.019 0.002 TRP B 659 HIS 0.025 0.002 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00480 (14030) covalent geometry : angle 0.72495 (19002) SS BOND : bond 0.00338 ( 36) SS BOND : angle 1.01552 ( 72) hydrogen bonds : bond 0.03981 ( 316) hydrogen bonds : angle 7.59655 ( 840) Misc. bond : bond 0.01014 ( 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 63 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.564 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: 0.9415 (tp) cc_final: 0.9157 (tt) REVERT: D 15 LEU cc_start: 0.9436 (tp) cc_final: 0.9184 (tt) REVERT: B 432 ASN cc_start: 0.8621 (m-40) cc_final: 0.8047 (p0) REVERT: B 606 TYR cc_start: 0.8600 (m-10) cc_final: 0.8339 (m-10) REVERT: A 136 LEU cc_start: 0.8941 (mt) cc_final: 0.8381 (pp) REVERT: A 432 ASN cc_start: 0.8654 (m-40) cc_final: 0.7465 (t0) REVERT: A 606 TYR cc_start: 0.8599 (m-10) cc_final: 0.8361 (m-10) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1103 time to fit residues: 11.2087 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 : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 42 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 364 ASN ** B 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** A 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.082605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.057396 restraints weight = 116505.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.057638 restraints weight = 79242.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.058109 restraints weight = 56380.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.058427 restraints weight = 46656.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.058617 restraints weight = 40470.969| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14068 Z= 0.145 Angle : 0.678 15.163 19074 Z= 0.352 Chirality : 0.047 0.233 2070 Planarity : 0.004 0.036 2454 Dihedral : 6.081 39.312 1858 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.20), residues: 1666 helix: -0.77 (0.36), residues: 200 sheet: -0.74 (0.31), residues: 272 loop : -1.62 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 581 TYR 0.020 0.002 TYR B 457 PHE 0.031 0.002 PHE A 454 TRP 0.013 0.001 TRP B 659 HIS 0.017 0.002 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00312 (14030) covalent geometry : angle 0.67133 (19002) SS BOND : bond 0.00204 ( 36) SS BOND : angle 1.71061 ( 72) hydrogen bonds : bond 0.03609 ( 316) hydrogen bonds : angle 7.44759 ( 840) Misc. bond : bond 0.00385 ( 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 68 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.595 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: 0.9367 (tp) cc_final: 0.9124 (tt) REVERT: D 15 LEU cc_start: 0.9379 (tp) cc_final: 0.9132 (tt) REVERT: B 136 LEU cc_start: 0.8771 (mt) cc_final: 0.8078 (pp) REVERT: B 432 ASN cc_start: 0.8622 (m-40) cc_final: 0.8035 (p0) REVERT: B 606 TYR cc_start: 0.8633 (m-10) cc_final: 0.8367 (m-10) REVERT: A 136 LEU cc_start: 0.8766 (mt) cc_final: 0.8154 (pp) REVERT: A 606 TYR cc_start: 0.8629 (m-10) cc_final: 0.8373 (m-10) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1070 time to fit residues: 11.9022 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 : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 163 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.088733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.060934 restraints weight = 116680.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.060035 restraints weight = 80872.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.060430 restraints weight = 58379.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.060703 restraints weight = 48952.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.060747 restraints weight = 41587.109| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14068 Z= 0.151 Angle : 0.699 14.382 19074 Z= 0.363 Chirality : 0.046 0.219 2070 Planarity : 0.004 0.037 2454 Dihedral : 6.081 38.905 1858 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.20), residues: 1666 helix: -0.66 (0.37), residues: 200 sheet: -0.64 (0.30), residues: 292 loop : -1.60 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 416 TYR 0.017 0.002 TYR A 457 PHE 0.017 0.002 PHE A 454 TRP 0.014 0.001 TRP B 659 HIS 0.028 0.002 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00325 (14030) covalent geometry : angle 0.69461 (19002) SS BOND : bond 0.00205 ( 36) SS BOND : angle 1.49135 ( 72) hydrogen bonds : bond 0.03543 ( 316) hydrogen bonds : angle 7.37455 ( 840) Misc. bond : bond 0.00974 ( 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 72 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.585 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: 0.9360 (tp) cc_final: 0.9117 (tt) REVERT: D 15 LEU cc_start: 0.9364 (tp) cc_final: 0.9119 (tt) REVERT: B 136 LEU cc_start: 0.8963 (mt) cc_final: 0.8316 (pp) REVERT: B 432 ASN cc_start: 0.8703 (m-40) cc_final: 0.8115 (p0) REVERT: B 606 TYR cc_start: 0.8640 (m-10) cc_final: 0.8385 (m-10) REVERT: A 136 LEU cc_start: 0.8896 (mt) cc_final: 0.8339 (pp) REVERT: A 606 TYR cc_start: 0.8610 (m-10) cc_final: 0.8344 (m-10) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1172 time to fit residues: 13.2768 Evaluate side-chains 55 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 69 optimal weight: 30.0000 chunk 36 optimal weight: 0.0980 chunk 137 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 161 optimal weight: 30.0000 chunk 7 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** A 456 HIS ** 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 = 0.4010 r_free = 0.4010 target = 0.089280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.062049 restraints weight = 116338.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.060875 restraints weight = 77883.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.061215 restraints weight = 57223.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.061325 restraints weight = 47184.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.061406 restraints weight = 42329.996| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.002 0.037 14068 Z= 0.114 Angle : 0.654 12.624 19074 Z= 0.338 Chirality : 0.046 0.214 2070 Planarity : 0.004 0.037 2454 Dihedral : 5.839 37.745 1858 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.20), residues: 1666 helix: -0.55 (0.36), residues: 200 sheet: -0.58 (0.30), residues: 292 loop : -1.58 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 416 TYR 0.030 0.001 TYR B 457 PHE 0.048 0.002 PHE A 454 TRP 0.014 0.001 TRP B 659 HIS 0.040 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00250 (14030) covalent geometry : angle 0.65008 (19002) SS BOND : bond 0.00149 ( 36) SS BOND : angle 1.38000 ( 72) hydrogen bonds : bond 0.03403 ( 316) hydrogen bonds : angle 7.22681 ( 840) Misc. bond : bond 0.00302 ( 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 71 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.603 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: 0.9279 (tp) cc_final: 0.9041 (tp) REVERT: D 15 LEU cc_start: 0.9282 (tp) cc_final: 0.9037 (tp) REVERT: B 136 LEU cc_start: 0.9060 (mt) cc_final: 0.8459 (pp) REVERT: B 432 ASN cc_start: 0.8784 (m-40) cc_final: 0.8078 (p0) REVERT: B 606 TYR cc_start: 0.8672 (m-10) cc_final: 0.8420 (m-10) REVERT: A 136 LEU cc_start: 0.9034 (mt) cc_final: 0.8479 (pp) REVERT: A 606 TYR cc_start: 0.8679 (m-10) cc_final: 0.8420 (m-10) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1151 time to fit residues: 13.0231 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 : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 107 optimal weight: 0.0030 chunk 67 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 163 optimal weight: 0.0970 chunk 86 optimal weight: 3.9990 chunk 104 optimal weight: 30.0000 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.088337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.061287 restraints weight = 117262.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.060007 restraints weight = 84469.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.060368 restraints weight = 58956.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.060585 restraints weight = 47503.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.060895 restraints weight = 39853.566| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4600 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= 0.151 Angle : 0.692 20.821 19074 Z= 0.355 Chirality : 0.045 0.213 2070 Planarity : 0.004 0.038 2454 Dihedral : 5.817 36.803 1858 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.20), residues: 1666 helix: -0.56 (0.37), residues: 202 sheet: -0.52 (0.32), residues: 272 loop : -1.58 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.050 0.002 TYR B 457 PHE 0.036 0.002 PHE A 454 TRP 0.018 0.001 TRP A 659 HIS 0.047 0.002 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00332 (14030) covalent geometry : angle 0.68903 (19002) SS BOND : bond 0.00190 ( 36) SS BOND : angle 1.31044 ( 72) hydrogen bonds : bond 0.03406 ( 316) hydrogen bonds : angle 7.19944 ( 840) Misc. bond : bond 0.00736 ( 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 69 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.520 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: 0.9363 (tp) cc_final: 0.9134 (tt) REVERT: D 15 LEU cc_start: 0.9359 (tp) cc_final: 0.9118 (tt) REVERT: B 136 LEU cc_start: 0.9080 (mt) cc_final: 0.8479 (pp) REVERT: B 432 ASN cc_start: 0.8809 (m-40) cc_final: 0.8088 (p0) REVERT: B 606 TYR cc_start: 0.8645 (m-10) cc_final: 0.8390 (m-10) REVERT: A 136 LEU cc_start: 0.9067 (mt) cc_final: 0.8502 (pp) REVERT: A 606 TYR cc_start: 0.8652 (m-10) cc_final: 0.8385 (m-10) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1212 time to fit residues: 13.1384 Evaluate side-chains 58 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 68 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 13 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.088610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.061855 restraints weight = 117175.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.060558 restraints weight = 86297.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.061168 restraints weight = 60811.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.061514 restraints weight = 47359.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.061484 restraints weight = 39594.988| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14068 Z= 0.129 Angle : 0.673 15.472 19074 Z= 0.345 Chirality : 0.046 0.215 2070 Planarity : 0.004 0.038 2454 Dihedral : 5.806 36.016 1858 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.20), residues: 1666 helix: -0.52 (0.37), residues: 202 sheet: -0.46 (0.32), residues: 272 loop : -1.57 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.019 0.002 TYR B 457 PHE 0.012 0.002 PHE A 455 TRP 0.016 0.001 TRP A 659 HIS 0.015 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00283 (14030) covalent geometry : angle 0.66993 (19002) SS BOND : bond 0.00162 ( 36) SS BOND : angle 1.26359 ( 72) hydrogen bonds : bond 0.03360 ( 316) hydrogen bonds : angle 7.13260 ( 840) Misc. bond : bond 0.00636 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4084.72 seconds wall clock time: 70 minutes 59.27 seconds (4259.27 seconds total)