Starting phenix.real_space_refine on Sat Oct 24 03:56:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s8d_10118/10_2026/6s8d_10118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8d_10118/10_2026/6s8d_10118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6s8d_10118/10_2026/6s8d_10118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8d_10118/10_2026/6s8d_10118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s8d_10118/10_2026/6s8d_10118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8d_10118/10_2026/6s8d_10118.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6s8d_10118/10_2026/6s8d_10118.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s8d_10118/10_2026/6s8d_10118.cif" } resolution = 3.49 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= 0.008 sd= 0.104 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 51 5.16 5 C 7782 2.51 5 N 2091 2.21 5 O 2343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12267 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: O, U, P, Y, C, E, D, F, I, J Time building chain proxies: 2.51, per 1000 atoms: 0.20 Number of scatterers: 12267 At special positions: 0 Unit cell: (100.182, 101.031, 123.105, 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 51 16.00 O 2343 8.00 N 2091 7.00 C 7782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.05 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.03 Simple disulfide: pdb=" SG CYS D 609 " - pdb=" SG CYS C 53 " distance=2.11 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS E 53 " distance=1.93 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 91 " distance=2.04 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 91 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 98 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 588.7 milliseconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2844 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 33 sheets defined 12.7% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.871A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.779A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 4.019A pdb=" N ILE B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.680A pdb=" N GLY B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.705A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 4.018A pdb=" N ILE D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.680A pdb=" N GLY D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.705A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 4.019A pdb=" N ILE F 542 " --> pdb=" O ALA F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.679A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.704A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.871A pdb=" N GLU O 86 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 86 removed outlier: 3.872A pdb=" N GLU U 86 " --> pdb=" O ALA U 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.779A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.779A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.480A pdb=" N TRP L 38 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS L 48 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR H 100 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 45 removed outlier: 7.133A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 42 through 45 removed outlier: 7.133A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.453A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AB4, first strand: chain 'D' and resid 580 through 581 removed outlier: 7.132A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 580 through 581 Processing sheet with id=AB6, first strand: chain 'F' and resid 544 through 548 Processing sheet with id=AB7, first strand: chain 'F' and resid 580 through 581 removed outlier: 7.133A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.480A pdb=" N TRP O 38 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS O 48 " --> pdb=" O GLN O 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'O' and resid 18 through 24 Processing sheet with id=AC3, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.479A pdb=" N TRP U 38 " --> pdb=" O ILE U 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS U 48 " --> pdb=" O GLN U 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 10 through 12 Processing sheet with id=AC5, first strand: chain 'U' and resid 18 through 24 Processing sheet with id=AC6, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC7, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.452A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AC9, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.452A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU E 112 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 136 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE E 218 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL E 138 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR E 220 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS E 140 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA E 222 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER E 142 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'P' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR P 100 " --> pdb=" O TYR P 113 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'Y' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR Y 100 " --> pdb=" O TYR Y 113 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.30 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: 3976 1.34 - 1.46: 2859 1.46 - 1.58: 5675 1.58 - 1.69: 3 1.69 - 1.81: 60 Bond restraints: 12573 Sorted by residual: bond pdb=" CB ILE D 527 " pdb=" CG2 ILE D 527 " ideal model delta sigma weight residual 1.521 1.584 -0.063 3.30e-02 9.18e+02 3.61e+00 bond pdb=" CB ILE F 527 " pdb=" CG2 ILE F 527 " ideal model delta sigma weight residual 1.521 1.583 -0.062 3.30e-02 9.18e+02 3.57e+00 bond pdb=" CB ILE B 527 " pdb=" CG2 ILE B 527 " ideal model delta sigma weight residual 1.521 1.583 -0.062 3.30e-02 9.18e+02 3.51e+00 bond pdb=" CB ILE D 527 " pdb=" CG1 ILE D 527 " ideal model delta sigma weight residual 1.530 1.559 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" CB ILE F 527 " pdb=" CG1 ILE F 527 " ideal model delta sigma weight residual 1.530 1.559 -0.029 2.00e-02 2.50e+03 2.06e+00 ... (remaining 12568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16516 1.99 - 3.99: 493 3.99 - 5.98: 82 5.98 - 7.97: 18 7.97 - 9.97: 3 Bond angle restraints: 17112 Sorted by residual: angle pdb=" N ILE F 527 " pdb=" CA ILE F 527 " pdb=" C ILE F 527 " ideal model delta sigma weight residual 106.53 113.33 -6.80 1.41e+00 5.03e-01 2.32e+01 angle pdb=" N ILE B 527 " pdb=" CA ILE B 527 " pdb=" C ILE B 527 " ideal model delta sigma weight residual 106.53 113.30 -6.77 1.41e+00 5.03e-01 2.30e+01 angle pdb=" N ILE D 527 " pdb=" CA ILE D 527 " pdb=" C ILE D 527 " ideal model delta sigma weight residual 106.53 113.29 -6.76 1.41e+00 5.03e-01 2.30e+01 angle pdb=" C ASP Y 92 " pdb=" N THR Y 93 " pdb=" CA THR Y 93 " ideal model delta sigma weight residual 122.85 127.48 -4.63 1.39e+00 5.18e-01 1.11e+01 angle pdb=" CG1 ILE B 527 " pdb=" CB ILE B 527 " pdb=" CG2 ILE B 527 " ideal model delta sigma weight residual 110.70 120.67 -9.97 3.00e+00 1.11e-01 1.10e+01 ... (remaining 17107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6640 17.85 - 35.70: 551 35.70 - 53.56: 105 53.56 - 71.41: 21 71.41 - 89.26: 15 Dihedral angle restraints: 7332 sinusoidal: 2835 harmonic: 4497 Sorted by residual: dihedral pdb=" CB CYS E 121 " pdb=" SG CYS E 121 " pdb=" SG CYS E 147 " pdb=" CB CYS E 147 " ideal model delta sinusoidal sigma weight residual -86.00 3.26 -89.26 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 147 " pdb=" CB CYS C 147 " ideal model delta sinusoidal sigma weight residual -86.00 3.25 -89.25 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 3.23 -89.23 1 1.00e+01 1.00e-02 9.47e+01 ... (remaining 7329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.327: 1866 0.327 - 0.655: 3 0.655 - 0.982: 0 0.982 - 1.309: 0 1.309 - 1.636: 3 Chirality restraints: 1872 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-02 2.50e+03 6.69e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-02 2.50e+03 6.69e+03 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-02 2.50e+03 6.69e+03 ... (remaining 1869 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA H 94 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C ALA H 94 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA H 94 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL H 95 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA P 94 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C ALA P 94 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA P 94 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL P 95 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 94 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C ALA Y 94 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA Y 94 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL Y 95 " -0.015 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2768 2.78 - 3.31: 10659 3.31 - 3.84: 18665 3.84 - 4.37: 21850 4.37 - 4.90: 39083 Nonbonded interactions: 93025 Sorted by model distance: nonbonded pdb=" O GLY O 80 " pdb=" NE2 GLN O 82 " model vdw 2.255 3.120 nonbonded pdb=" O GLY U 80 " pdb=" NE2 GLN U 82 " model vdw 2.255 3.120 nonbonded pdb=" O GLY L 80 " pdb=" NE2 GLN L 82 " model vdw 2.256 3.120 nonbonded pdb=" OD2 ASP L 100 " pdb=" OG1 THR A 144 " model vdw 2.287 3.040 nonbonded pdb=" O SER U 3 " pdb=" OG SER U 3 " model vdw 2.324 3.040 ... (remaining 93020 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: 0.04 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.820 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.006 0.106 12600 Z= 0.257 Angle : 1.094 44.784 17172 Z= 0.522 Chirality : 0.085 1.636 1872 Planarity : 0.005 0.043 2217 Dihedral : 13.812 88.998 4425 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.25 % Favored : 95.56 % Rotamer: Outliers : 2.56 % Allowed : 4.74 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.20), residues: 1554 helix: 0.45 (0.43), residues: 126 sheet: -0.17 (0.20), residues: 624 loop : -1.03 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 559 TYR 0.021 0.002 TYR P 97 PHE 0.014 0.002 PHE C 132 TRP 0.011 0.001 TRP D 597 HIS 0.004 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 (12573) covalent geometry : angle 0.85068 / 0.47 (17112) SS BOND : bond 0.02903 / 1.84 ( 21) SS BOND : angle 2.29635 / 1.49 ( 42) hydrogen bonds : bond 0.15875 / 11.05 ( 397) hydrogen bonds : angle 7.63916 / 5.29 ( 1149) link_BETA1-4 : bond 0.06526 / 3.27 ( 3) link_BETA1-4 : angle 29.67574 / 14.79 ( 9) link_NAG-ASN : bond 0.00458 / 0.23 ( 3) link_NAG-ASN : angle 1.45233 / 0.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8253 (m-30) cc_final: 0.8007 (m-30) REVERT: P 3 GLN cc_start: 0.7395 (tm-30) cc_final: 0.6999 (tm-30) outliers start: 33 outliers final: 12 residues processed: 282 average time/residue: 0.1139 time to fit residues: 45.5224 Evaluate side-chains 202 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain E residue 229 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 56 ASN A 39 HIS A 61 ASN B 516 HIS D 516 HIS O 56 ASN U 56 ASN C 39 HIS C 61 ASN E 39 HIS E 61 ASN E 188 GLN P 35 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.192886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156544 restraints weight = 14777.154| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.46 r_work: 0.3505 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12600 Z= 0.173 Angle : 0.659 6.255 17172 Z= 0.346 Chirality : 0.045 0.156 1872 Planarity : 0.005 0.042 2217 Dihedral : 6.691 89.889 1755 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.80 % Allowed : 12.28 % Favored : 84.93 % 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 are not related in a simple way. whole: -0.41 (0.21), residues: 1554 helix: 1.40 (0.47), residues: 126 sheet: 0.10 (0.20), residues: 636 loop : -0.82 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 172 TYR 0.012 0.001 TYR Y 62 PHE 0.020 0.002 PHE D 592 TRP 0.008 0.001 TRP E 104 HIS 0.004 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (12573) covalent geometry : angle 0.65114 / 0.34 (17112) SS BOND : bond 0.00293 / 0.18 ( 21) SS BOND : angle 1.63090 / 1.02 ( 42) hydrogen bonds : bond 0.05496 / 3.80 ( 397) hydrogen bonds : angle 5.41724 / 3.75 ( 1149) link_BETA1-4 : bond 0.00244 / 0.13 ( 3) link_BETA1-4 : angle 2.50542 / 1.26 ( 9) link_NAG-ASN : bond 0.00144 / 0.07 ( 3) link_NAG-ASN : angle 1.70745 / 0.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 ASP cc_start: 0.8329 (m-30) cc_final: 0.8092 (m-30) REVERT: H 19 ARG cc_start: 0.7166 (ttm170) cc_final: 0.6218 (ttm170) REVERT: D 510 LYS cc_start: 0.7370 (mppt) cc_final: 0.7124 (mppt) REVERT: D 596 ARG cc_start: 0.8528 (mtt90) cc_final: 0.8281 (mtt90) REVERT: F 545 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7309 (mt-10) REVERT: O 97 ARG cc_start: 0.8232 (mtm-85) cc_final: 0.7924 (mtm-85) REVERT: C 228 ASN cc_start: 0.8454 (t0) cc_final: 0.8221 (t0) REVERT: P 3 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7280 (tm-30) REVERT: P 18 LEU cc_start: 0.8054 (tp) cc_final: 0.7657 (mp) REVERT: Y 19 ARG cc_start: 0.7712 (ttt-90) cc_final: 0.7315 (ttt90) outliers start: 36 outliers final: 22 residues processed: 226 average time/residue: 0.1091 time to fit residues: 35.1728 Evaluate side-chains 209 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [134, 139, 125, 25, 148, 33, 150, 83, 122, 39, 129] chunk 134 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 150 optimal weight: 0.0170 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 29 ASN U 29 ASN C 188 GLN E 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.191609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.153968 restraints weight = 14816.273| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.50 r_work: 0.3491 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12600 Z= 0.120 Angle : 0.580 6.145 17172 Z= 0.302 Chirality : 0.043 0.149 1872 Planarity : 0.004 0.045 2217 Dihedral : 5.127 39.802 1742 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.03 % Allowed : 13.91 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1554 helix: 1.64 (0.49), residues: 126 sheet: 0.12 (0.21), residues: 615 loop : -0.69 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 97 TYR 0.011 0.001 TYR H 97 PHE 0.020 0.001 PHE H 29 TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS P 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (12573) covalent geometry : angle 0.57460 / 0.30 (17112) SS BOND : bond 0.00280 / 0.16 ( 21) SS BOND : angle 1.27345 / 0.76 ( 42) hydrogen bonds : bond 0.04498 / 3.07 ( 397) hydrogen bonds : angle 4.90692 / 3.38 ( 1149) link_BETA1-4 : bond 0.00414 / 0.21 ( 3) link_BETA1-4 : angle 2.16989 / 1.13 ( 9) link_NAG-ASN : bond 0.00227 / 0.11 ( 3) link_NAG-ASN : angle 0.87628 / 0.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7083 (ttm170) cc_final: 0.6129 (ttm170) REVERT: D 596 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8220 (mtt90) REVERT: F 591 ASP cc_start: 0.8490 (m-30) cc_final: 0.8286 (m-30) REVERT: O 97 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.8088 (mtm-85) REVERT: C 228 ASN cc_start: 0.8521 (t0) cc_final: 0.8271 (t0) REVERT: E 228 ASN cc_start: 0.8574 (t0) cc_final: 0.8262 (t0) REVERT: P 3 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7451 (tm-30) outliers start: 39 outliers final: 25 residues processed: 222 average time/residue: 0.1050 time to fit residues: 34.0918 Evaluate side-chains 216 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [39, 17, 153, 65, 2, 23, 36, 125, 43, 37, 102] chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 29 ASN H 3 GLN A 188 GLN U 29 ASN C 188 GLN E 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.187362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148776 restraints weight = 15125.588| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.76 r_work: 0.3386 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12600 Z= 0.226 Angle : 0.646 6.796 17172 Z= 0.338 Chirality : 0.045 0.147 1872 Planarity : 0.005 0.046 2217 Dihedral : 5.164 38.962 1741 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.50 % Allowed : 14.61 % Favored : 81.90 % 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 are not related in a simple way. whole: -0.42 (0.21), residues: 1554 helix: 1.20 (0.48), residues: 126 sheet: 0.08 (0.21), residues: 582 loop : -0.73 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 97 TYR 0.018 0.002 TYR H 97 PHE 0.020 0.002 PHE B 592 TRP 0.012 0.001 TRP H 36 HIS 0.003 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 (12573) covalent geometry : angle 0.64007 / 0.34 (17112) SS BOND : bond 0.00414 / 0.29 ( 21) SS BOND : angle 1.54890 / 0.96 ( 42) hydrogen bonds : bond 0.05081 / 3.48 ( 397) hydrogen bonds : angle 4.91763 / 3.38 ( 1149) link_BETA1-4 : bond 0.00343 / 0.17 ( 3) link_BETA1-4 : angle 2.05065 / 1.07 ( 9) link_NAG-ASN : bond 0.00080 / 0.04 ( 3) link_NAG-ASN : angle 0.97121 / 0.48 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7116 (ttm170) cc_final: 0.6093 (ttm170) REVERT: D 596 ARG cc_start: 0.8579 (mtt90) cc_final: 0.8212 (mtt90) REVERT: C 228 ASN cc_start: 0.8535 (t0) cc_final: 0.8179 (t0) REVERT: E 228 ASN cc_start: 0.8568 (t0) cc_final: 0.8268 (t0) REVERT: P 18 LEU cc_start: 0.8036 (tp) cc_final: 0.7739 (mt) REVERT: P 84 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8169 (mm-40) REVERT: Y 29 PHE cc_start: 0.8219 (t80) cc_final: 0.8011 (t80) outliers start: 45 outliers final: 33 residues processed: 229 average time/residue: 0.1051 time to fit residues: 34.5475 Evaluate side-chains 231 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [67, 66, 57, 0, 4, 45, 103, 47, 14, 85, 147] chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 29 ASN A 188 GLN C 188 GLN E 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.196022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156473 restraints weight = 15173.623| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.63 r_work: 0.3444 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12600 Z= 0.130 Angle : 0.573 5.972 17172 Z= 0.300 Chirality : 0.043 0.144 1872 Planarity : 0.004 0.043 2217 Dihedral : 4.975 38.946 1739 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.34 % Allowed : 15.54 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1554 helix: 1.54 (0.49), residues: 126 sheet: 0.02 (0.21), residues: 585 loop : -0.66 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 97 TYR 0.013 0.001 TYR H 97 PHE 0.016 0.001 PHE H 29 TRP 0.010 0.001 TRP H 36 HIS 0.002 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (12573) covalent geometry : angle 0.56854 / 0.30 (17112) SS BOND : bond 0.00240 / 0.16 ( 21) SS BOND : angle 1.14915 / 0.79 ( 42) hydrogen bonds : bond 0.04328 / 2.93 ( 397) hydrogen bonds : angle 4.72116 / 3.25 ( 1149) link_BETA1-4 : bond 0.00323 / 0.16 ( 3) link_BETA1-4 : angle 2.03363 / 1.07 ( 9) link_NAG-ASN : bond 0.00108 / 0.06 ( 3) link_NAG-ASN : angle 0.78634 / 0.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7041 (ttm170) cc_final: 0.6111 (ttm170) REVERT: H 61 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6700 (m-30) REVERT: A 120 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7639 (tp30) REVERT: A 228 ASN cc_start: 0.8521 (t0) cc_final: 0.8263 (t0) REVERT: D 596 ARG cc_start: 0.8535 (mtt90) cc_final: 0.8274 (mtt90) REVERT: C 188 GLN cc_start: 0.6120 (tp40) cc_final: 0.5781 (tp-100) REVERT: C 228 ASN cc_start: 0.8496 (t0) cc_final: 0.8142 (t0) REVERT: E 228 ASN cc_start: 0.8542 (t0) cc_final: 0.8222 (t0) outliers start: 43 outliers final: 33 residues processed: 233 average time/residue: 0.1073 time to fit residues: 36.3965 Evaluate side-chains 234 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [135, 62, 88, 91, 114, 149, 155, 66, 32, 151, 45] chunk 135 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 ASN A 188 GLN E 39 HIS E 188 GLN ** P 84 GLN ** 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 = 0.4151 r_free = 0.4151 target = 0.186225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147572 restraints weight = 15210.957| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.71 r_work: 0.3370 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12600 Z= 0.219 Angle : 0.628 7.457 17172 Z= 0.328 Chirality : 0.045 0.143 1872 Planarity : 0.005 0.044 2217 Dihedral : 4.997 39.369 1739 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.81 % Allowed : 16.01 % Favored : 80.19 % 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 are not related in a simple way. whole: -0.43 (0.21), residues: 1554 helix: 1.16 (0.48), residues: 126 sheet: 0.25 (0.22), residues: 543 loop : -0.84 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 19 TYR 0.018 0.002 TYR H 97 PHE 0.019 0.002 PHE F 592 TRP 0.010 0.001 TRP H 36 HIS 0.003 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (12573) covalent geometry : angle 0.62330 / 0.33 (17112) SS BOND : bond 0.00296 / 0.19 ( 21) SS BOND : angle 1.31487 / 0.86 ( 42) hydrogen bonds : bond 0.04960 / 3.40 ( 397) hydrogen bonds : angle 4.72883 / 3.28 ( 1149) link_BETA1-4 : bond 0.00392 / 0.20 ( 3) link_BETA1-4 : angle 1.98957 / 1.05 ( 9) link_NAG-ASN : bond 0.00107 / 0.05 ( 3) link_NAG-ASN : angle 0.83462 / 0.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7181 (ttm170) cc_final: 0.6189 (ttm170) REVERT: A 228 ASN cc_start: 0.8581 (t0) cc_final: 0.8357 (t0) REVERT: D 596 ARG cc_start: 0.8558 (mtt90) cc_final: 0.8287 (mtt90) REVERT: F 545 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7502 (mt-10) REVERT: U 51 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8097 (mt) REVERT: C 188 GLN cc_start: 0.6203 (tp40) cc_final: 0.5647 (mm-40) REVERT: C 228 ASN cc_start: 0.8580 (t0) cc_final: 0.8200 (t0) REVERT: E 228 ASN cc_start: 0.8504 (t0) cc_final: 0.8182 (t0) REVERT: P 18 LEU cc_start: 0.7801 (tp) cc_final: 0.7552 (mt) outliers start: 49 outliers final: 32 residues processed: 230 average time/residue: 0.1073 time to fit residues: 35.5546 Evaluate side-chains 230 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [27, 52, 56, 79, 22, 74, 149, 122, 47, 45, 37] chunk 27 optimal weight: 0.0070 chunk 52 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.189731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.153020 restraints weight = 15123.186| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.56 r_work: 0.3454 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12600 Z= 0.115 Angle : 0.570 7.959 17172 Z= 0.298 Chirality : 0.043 0.175 1872 Planarity : 0.004 0.046 2217 Dihedral : 4.822 39.084 1739 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.95 % Allowed : 16.94 % Favored : 80.11 % 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 are not related in a simple way. whole: -0.38 (0.21), residues: 1554 helix: 1.65 (0.49), residues: 126 sheet: -0.02 (0.21), residues: 591 loop : -0.68 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 19 TYR 0.012 0.001 TYR H 97 PHE 0.014 0.001 PHE F 592 TRP 0.008 0.001 TRP H 36 HIS 0.002 0.000 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (12573) covalent geometry : angle 0.56522 / 0.30 (17112) SS BOND : bond 0.00304 / 0.17 ( 21) SS BOND : angle 1.23584 / 0.74 ( 42) hydrogen bonds : bond 0.04096 / 2.77 ( 397) hydrogen bonds : angle 4.55292 / 3.15 ( 1149) link_BETA1-4 : bond 0.00351 / 0.18 ( 3) link_BETA1-4 : angle 1.97951 / 1.05 ( 9) link_NAG-ASN : bond 0.00116 / 0.06 ( 3) link_NAG-ASN : angle 0.79875 / 0.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8207 (m-30) cc_final: 0.7951 (m-30) REVERT: H 19 ARG cc_start: 0.7099 (ttm170) cc_final: 0.6135 (ttm170) REVERT: H 61 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: D 596 ARG cc_start: 0.8487 (mtt90) cc_final: 0.8256 (mtt90) REVERT: U 51 ILE cc_start: 0.8347 (mm) cc_final: 0.8133 (mt) REVERT: U 97 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: C 188 GLN cc_start: 0.6171 (tp40) cc_final: 0.5670 (mm-40) REVERT: C 228 ASN cc_start: 0.8544 (t0) cc_final: 0.8216 (t0) REVERT: E 120 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7596 (mt-10) REVERT: E 228 ASN cc_start: 0.8515 (t0) cc_final: 0.8232 (t0) REVERT: P 19 ARG cc_start: 0.7845 (ttt-90) cc_final: 0.7600 (tpt-90) outliers start: 38 outliers final: 31 residues processed: 224 average time/residue: 0.1095 time to fit residues: 35.3565 Evaluate side-chains 222 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [136, 152, 56, 90, 40, 149, 81, 73, 69, 25, 18] chunk 136 optimal weight: 0.5980 chunk 152 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.184922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146930 restraints weight = 15191.127| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.93 r_work: 0.3348 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12600 Z= 0.257 Angle : 0.675 7.025 17172 Z= 0.351 Chirality : 0.046 0.147 1872 Planarity : 0.005 0.062 2217 Dihedral : 5.022 39.408 1737 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.26 % Allowed : 17.64 % Favored : 79.10 % 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 are not related in a simple way. whole: -0.51 (0.21), residues: 1554 helix: 1.09 (0.48), residues: 126 sheet: 0.25 (0.22), residues: 540 loop : -0.92 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 97 TYR 0.020 0.002 TYR H 97 PHE 0.021 0.002 PHE F 592 TRP 0.010 0.001 TRP P 36 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.26 (12573) covalent geometry : angle 0.66919 / 0.35 (17112) SS BOND : bond 0.00414 / 0.27 ( 21) SS BOND : angle 1.59415 / 0.94 ( 42) hydrogen bonds : bond 0.05146 / 3.53 ( 397) hydrogen bonds : angle 4.70109 / 3.27 ( 1149) link_BETA1-4 : bond 0.00368 / 0.18 ( 3) link_BETA1-4 : angle 2.01994 / 1.07 ( 9) link_NAG-ASN : bond 0.00196 / 0.10 ( 3) link_NAG-ASN : angle 0.93410 / 0.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.8273 (t80) REVERT: H 19 ARG cc_start: 0.7215 (ttm170) cc_final: 0.6183 (ttm170) REVERT: A 120 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 228 ASN cc_start: 0.8676 (t0) cc_final: 0.8423 (t0) REVERT: D 596 ARG cc_start: 0.8546 (mtt90) cc_final: 0.8010 (mtt90) REVERT: U 109 LYS cc_start: 0.7136 (tppt) cc_final: 0.6727 (tppt) REVERT: C 188 GLN cc_start: 0.6265 (tp40) cc_final: 0.5741 (mm-40) REVERT: C 228 ASN cc_start: 0.8589 (t0) cc_final: 0.8321 (t0) REVERT: E 188 GLN cc_start: 0.6256 (tp40) cc_final: 0.5848 (mm-40) REVERT: E 228 ASN cc_start: 0.8537 (t0) cc_final: 0.8333 (t0) REVERT: P 18 LEU cc_start: 0.8133 (tp) cc_final: 0.7558 (mt) REVERT: P 84 GLN cc_start: 0.8471 (tp40) cc_final: 0.7961 (mp10) REVERT: Y 18 LEU cc_start: 0.8093 (tp) cc_final: 0.7586 (mp) REVERT: Y 82 TYR cc_start: 0.8034 (m-80) cc_final: 0.7763 (m-80) outliers start: 42 outliers final: 34 residues processed: 224 average time/residue: 0.1100 time to fit residues: 35.2285 Evaluate side-chains 223 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [70, 99, 121, 128, 117, 10, 64, 61, 30, 36, 148] chunk 70 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.189598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.151512 restraints weight = 15077.905| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.73 r_work: 0.3442 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12600 Z= 0.117 Angle : 0.588 7.512 17172 Z= 0.307 Chirality : 0.043 0.206 1872 Planarity : 0.004 0.043 2217 Dihedral : 4.561 39.124 1733 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.56 % Allowed : 17.87 % Favored : 79.56 % 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 are not related in a simple way. whole: -0.41 (0.21), residues: 1554 helix: 1.57 (0.49), residues: 126 sheet: 0.01 (0.22), residues: 588 loop : -0.72 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 19 TYR 0.021 0.001 TYR P 82 PHE 0.015 0.001 PHE Y 29 TRP 0.009 0.001 TRP H 36 HIS 0.002 0.000 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (12573) covalent geometry : angle 0.58388 / 0.31 (17112) SS BOND : bond 0.00256 / 0.16 ( 21) SS BOND : angle 1.23098 / 0.69 ( 42) hydrogen bonds : bond 0.03988 / 2.69 ( 397) hydrogen bonds : angle 4.52567 / 3.13 ( 1149) link_BETA1-4 : bond 0.00335 / 0.17 ( 3) link_BETA1-4 : angle 2.01844 / 1.07 ( 9) link_NAG-ASN : bond 0.00139 / 0.07 ( 3) link_NAG-ASN : angle 0.88412 / 0.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8209 (m-30) cc_final: 0.7885 (m-30) REVERT: H 85 MET cc_start: 0.7068 (pmm) cc_final: 0.6810 (pmm) REVERT: A 228 ASN cc_start: 0.8541 (t0) cc_final: 0.8258 (t0) REVERT: B 596 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8099 (mtt90) REVERT: D 596 ARG cc_start: 0.8482 (mtt90) cc_final: 0.7834 (mtt90) REVERT: C 188 GLN cc_start: 0.6239 (tp40) cc_final: 0.5774 (mm-40) REVERT: C 228 ASN cc_start: 0.8553 (t0) cc_final: 0.8199 (t0) REVERT: E 188 GLN cc_start: 0.6149 (tp40) cc_final: 0.5799 (mm-40) REVERT: E 228 ASN cc_start: 0.8507 (t0) cc_final: 0.8226 (t0) REVERT: P 18 LEU cc_start: 0.7985 (tp) cc_final: 0.7112 (mt) REVERT: P 84 GLN cc_start: 0.8398 (tp40) cc_final: 0.7956 (mp10) REVERT: Y 18 LEU cc_start: 0.7996 (tp) cc_final: 0.7461 (mp) REVERT: Y 82 TYR cc_start: 0.7905 (m-80) cc_final: 0.7644 (m-80) outliers start: 33 outliers final: 27 residues processed: 228 average time/residue: 0.1089 time to fit residues: 35.4917 Evaluate side-chains 227 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [77, 0, 78, 92, 121, 132, 15, 57, 72, 125, 4] chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 15 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 516 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.184972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147455 restraints weight = 15252.794| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.90 r_work: 0.3357 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 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 0.042 12600 Z= 0.245 Angle : 0.678 8.258 17172 Z= 0.354 Chirality : 0.046 0.191 1872 Planarity : 0.005 0.051 2217 Dihedral : 4.619 18.528 1731 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.64 % Allowed : 18.49 % Favored : 78.87 % 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 are not related in a simple way. whole: -0.54 (0.21), residues: 1554 helix: 1.09 (0.49), residues: 126 sheet: 0.26 (0.23), residues: 531 loop : -0.96 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 97 TYR 0.024 0.002 TYR P 82 PHE 0.018 0.002 PHE Y 29 TRP 0.013 0.001 TRP P 36 HIS 0.003 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.25 (12573) covalent geometry : angle 0.67351 / 0.35 (17112) SS BOND : bond 0.00317 / 0.19 ( 21) SS BOND : angle 1.45712 / 0.88 ( 42) hydrogen bonds : bond 0.04969 / 3.39 ( 397) hydrogen bonds : angle 4.65465 / 3.23 ( 1149) link_BETA1-4 : bond 0.00266 / 0.13 ( 3) link_BETA1-4 : angle 2.05109 / 1.09 ( 9) link_NAG-ASN : bond 0.00206 / 0.10 ( 3) link_NAG-ASN : angle 1.01169 / 0.52 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 85 MET cc_start: 0.6935 (pmm) cc_final: 0.6674 (pmm) REVERT: A 228 ASN cc_start: 0.8574 (t0) cc_final: 0.8280 (t0) REVERT: B 596 ARG cc_start: 0.8900 (mtm-85) cc_final: 0.8438 (mtt90) REVERT: D 596 ARG cc_start: 0.8554 (mtt90) cc_final: 0.7990 (mtt90) REVERT: C 188 GLN cc_start: 0.6340 (tp40) cc_final: 0.5834 (mm-40) REVERT: C 228 ASN cc_start: 0.8557 (t0) cc_final: 0.8286 (t0) REVERT: E 188 GLN cc_start: 0.6241 (tp40) cc_final: 0.5873 (mm-40) REVERT: E 228 ASN cc_start: 0.8498 (t0) cc_final: 0.8259 (t0) REVERT: P 18 LEU cc_start: 0.7968 (tp) cc_final: 0.7740 (mt) REVERT: P 82 TYR cc_start: 0.7923 (m-10) cc_final: 0.7530 (m-10) REVERT: P 84 GLN cc_start: 0.8330 (tp40) cc_final: 0.7968 (mp10) REVERT: Y 18 LEU cc_start: 0.7930 (tp) cc_final: 0.7504 (mt) REVERT: Y 82 TYR cc_start: 0.8058 (m-80) cc_final: 0.7835 (m-80) outliers start: 34 outliers final: 32 residues processed: 211 average time/residue: 0.1115 time to fit residues: 33.4595 Evaluate side-chains 217 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [20, 100, 57, 3, 102, 86, 26, 79, 14, 32, 42] chunk 20 optimal weight: 3.9990 chunk 100 optimal weight: 0.0020 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.189243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.150508 restraints weight = 15087.958| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.79 r_work: 0.3422 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12600 Z= 0.119 Angle : 0.591 8.289 17172 Z= 0.307 Chirality : 0.043 0.150 1872 Planarity : 0.004 0.040 2217 Dihedral : 4.398 18.492 1731 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.25 % Allowed : 18.65 % Favored : 79.10 % 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 are not related in a simple way. whole: -0.47 (0.21), residues: 1554 helix: 1.58 (0.49), residues: 126 sheet: -0.02 (0.22), residues: 579 loop : -0.77 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 97 TYR 0.018 0.001 TYR P 82 PHE 0.013 0.001 PHE H 29 TRP 0.010 0.001 TRP H 36 HIS 0.002 0.001 HIS B 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (12573) covalent geometry : angle 0.58559 / 0.31 (17112) SS BOND : bond 0.00317 / 0.23 ( 21) SS BOND : angle 1.40840 / 0.98 ( 42) hydrogen bonds : bond 0.03968 / 2.67 ( 397) hydrogen bonds : angle 4.51049 / 3.12 ( 1149) link_BETA1-4 : bond 0.00335 / 0.17 ( 3) link_BETA1-4 : angle 2.01927 / 1.07 ( 9) link_NAG-ASN : bond 0.00105 / 0.05 ( 3) link_NAG-ASN : angle 0.89675 / 0.43 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.32 seconds wall clock time: 45 minutes 11.36 seconds (2711.36 seconds total)