Starting phenix.real_space_refine on Fri Sep 11 23:21:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s8d_10118/09_2026/6s8d_10118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8d_10118/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6s8d_10118/09_2026/6s8d_10118.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s8d_10118/09_2026/6s8d_10118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s8d_10118/09_2026/6s8d_10118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8d_10118/09_2026/6s8d_10118.map" model { file = "/net/cci-nas-00/data/ceres_data/6s8d_10118/09_2026/6s8d_10118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8d_10118/09_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-2.2.1-6174/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: 2.78, per 1000 atoms: 0.23 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 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 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 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS D 609 " distance=2.11 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS F 609 " distance=1.93 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 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 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.03 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG 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: 1.05 Conformation dependent library (CDL) restraints added in 634.9 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: 0.45 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: 2.15 Time building geometry restraints manager: 1.41 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: 553 35.70 - 53.56: 103 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- 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 / 1.54 ( 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 : 0.510 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: 0.1225 time to fit residues: 48.8756 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 : 0.454 ------------------------------------------------------------------------------- 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: 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 = 0.156545 restraints weight = 14777.147| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.46 r_work: 0.3499 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 89.890 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 / 1.04 ( 42) hydrogen bonds : bond 0.05496 / 3.80 ( 397) hydrogen bonds : angle 5.41722 / 3.75 ( 1149) link_BETA1-4 : bond 0.00245 / 0.13 ( 3) link_BETA1-4 : angle 2.50563 / 1.26 ( 9) link_NAG-ASN : bond 0.00145 / 0.07 ( 3) link_NAG-ASN : angle 1.70749 / 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 : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 ASP cc_start: 0.8325 (m-30) cc_final: 0.8089 (m-30) REVERT: H 19 ARG cc_start: 0.7162 (ttm170) cc_final: 0.6218 (ttm170) REVERT: D 510 LYS cc_start: 0.7356 (mppt) cc_final: 0.7120 (mppt) REVERT: D 596 ARG cc_start: 0.8520 (mtt90) cc_final: 0.8273 (mtt90) REVERT: F 545 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7317 (mt-10) REVERT: O 97 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7903 (mtm-85) REVERT: C 228 ASN cc_start: 0.8428 (t0) cc_final: 0.8192 (t0) REVERT: P 3 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7266 (tm-30) REVERT: P 18 LEU cc_start: 0.8060 (tp) cc_final: 0.7656 (mp) REVERT: Y 19 ARG cc_start: 0.7717 (ttt-90) cc_final: 0.7326 (ttt90) outliers start: 36 outliers final: 22 residues processed: 226 average time/residue: 0.1202 time to fit residues: 38.6809 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 : 0.448 ------------------------------------------------------------------------------- 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: chunk 134 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.191682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155852 restraints weight = 14832.240| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.48 r_work: 0.3488 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12600 Z= 0.163 Angle : 0.609 6.333 17172 Z= 0.318 Chirality : 0.044 0.147 1872 Planarity : 0.004 0.051 2217 Dihedral : 5.192 40.015 1742 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.34 % Allowed : 13.52 % Favored : 83.14 % 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: -0.40 (0.21), residues: 1554 helix: 1.39 (0.49), residues: 126 sheet: 0.07 (0.21), residues: 615 loop : -0.76 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 19 TYR 0.014 0.001 TYR H 97 PHE 0.020 0.002 PHE H 29 TRP 0.006 0.001 TRP H 36 HIS 0.003 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (12573) covalent geometry : angle 0.60324 / 0.32 (17112) SS BOND : bond 0.00277 / 0.17 ( 21) SS BOND : angle 1.37923 / 0.85 ( 42) hydrogen bonds : bond 0.04835 / 3.31 ( 397) hydrogen bonds : angle 4.95109 / 3.41 ( 1149) link_BETA1-4 : bond 0.00348 / 0.18 ( 3) link_BETA1-4 : angle 2.17840 / 1.14 ( 9) link_NAG-ASN : bond 0.00092 / 0.05 ( 3) link_NAG-ASN : angle 1.05488 / 0.50 ( 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 260 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7139 (ttm170) cc_final: 0.6147 (ttm170) REVERT: D 596 ARG cc_start: 0.8514 (mtt90) cc_final: 0.8186 (mtt90) REVERT: C 228 ASN cc_start: 0.8515 (t0) cc_final: 0.8250 (t0) REVERT: E 120 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7672 (mt-10) REVERT: E 172 ARG cc_start: 0.8669 (ttm170) cc_final: 0.8294 (ttm170) REVERT: E 228 ASN cc_start: 0.8564 (t0) cc_final: 0.8231 (t0) REVERT: P 3 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7442 (tm-30) outliers start: 43 outliers final: 29 residues processed: 237 average time/residue: 0.1175 time to fit residues: 40.0349 Evaluate side-chains 229 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 61 ASP 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 175 THR Chi-restraints excluded: chain A residue 227 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 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 U residue 99 SER Chi-restraints excluded: chain C residue 175 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 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: chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 43 optimal weight: 0.0040 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.189356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150956 restraints weight = 15126.549| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.72 r_work: 0.3432 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12600 Z= 0.158 Angle : 0.596 5.983 17172 Z= 0.312 Chirality : 0.044 0.141 1872 Planarity : 0.004 0.042 2217 Dihedral : 5.065 38.747 1740 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.34 % Allowed : 15.23 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.35 (0.21), residues: 1554 helix: 1.43 (0.49), residues: 126 sheet: 0.07 (0.21), residues: 582 loop : -0.66 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 97 TYR 0.014 0.001 TYR H 97 PHE 0.017 0.002 PHE Y 29 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 0.00381 / 0.16 (12573) covalent geometry : angle 0.59095 / 0.31 (17112) SS BOND : bond 0.00305 / 0.20 ( 21) SS BOND : angle 1.38173 / 0.94 ( 42) hydrogen bonds : bond 0.04590 / 3.13 ( 397) hydrogen bonds : angle 4.81937 / 3.31 ( 1149) link_BETA1-4 : bond 0.00347 / 0.17 ( 3) link_BETA1-4 : angle 2.04231 / 1.07 ( 9) link_NAG-ASN : bond 0.00070 / 0.04 ( 3) link_NAG-ASN : angle 0.92122 / 0.44 ( 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 251 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7080 (ttm170) cc_final: 0.6105 (ttm170) REVERT: A 120 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7626 (tp30) REVERT: D 596 ARG cc_start: 0.8539 (mtt90) cc_final: 0.8162 (mtt90) REVERT: U 97 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.8152 (mtm-85) REVERT: C 228 ASN cc_start: 0.8547 (t0) cc_final: 0.8207 (t0) REVERT: E 120 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7833 (mt-10) REVERT: E 228 ASN cc_start: 0.8562 (t0) cc_final: 0.8260 (t0) REVERT: P 18 LEU cc_start: 0.7983 (tp) cc_final: 0.7675 (mt) outliers start: 43 outliers final: 30 residues processed: 228 average time/residue: 0.1159 time to fit residues: 38.0913 Evaluate side-chains 229 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 48 VAL 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 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 U residue 29 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 102 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.0070 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN C 188 GLN E 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.190158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.152036 restraints weight = 15223.470| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.74 r_work: 0.3437 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12600 Z= 0.127 Angle : 0.557 5.859 17172 Z= 0.292 Chirality : 0.043 0.140 1872 Planarity : 0.004 0.043 2217 Dihedral : 4.857 39.245 1739 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.57 % Allowed : 15.15 % Favored : 81.27 % 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: -0.35 (0.21), residues: 1554 helix: 1.59 (0.49), residues: 126 sheet: 0.01 (0.21), residues: 591 loop : -0.64 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 97 TYR 0.013 0.001 TYR H 97 PHE 0.016 0.002 PHE H 29 TRP 0.009 0.001 TRP H 36 HIS 0.002 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (12573) covalent geometry : angle 0.55323 / 0.29 (17112) SS BOND : bond 0.00349 / 0.27 ( 21) SS BOND : angle 1.04059 / 0.69 ( 42) hydrogen bonds : bond 0.04173 / 2.82 ( 397) hydrogen bonds : angle 4.60475 / 3.16 ( 1149) link_BETA1-4 : bond 0.00356 / 0.18 ( 3) link_BETA1-4 : angle 2.00812 / 1.06 ( 9) link_NAG-ASN : bond 0.00078 / 0.04 ( 3) link_NAG-ASN : angle 0.78175 / 0.37 ( 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 261 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7040 (ttm170) cc_final: 0.6112 (ttm170) REVERT: A 120 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7590 (tp30) REVERT: A 228 ASN cc_start: 0.8575 (t0) cc_final: 0.8294 (t0) REVERT: D 596 ARG cc_start: 0.8531 (mtt90) cc_final: 0.8249 (mtt90) REVERT: C 188 GLN cc_start: 0.6108 (tp40) cc_final: 0.5802 (tp-100) REVERT: C 228 ASN cc_start: 0.8523 (t0) cc_final: 0.8174 (t0) REVERT: E 228 ASN cc_start: 0.8467 (t0) cc_final: 0.8157 (t0) REVERT: P 18 LEU cc_start: 0.7888 (tp) cc_final: 0.7542 (mt) REVERT: P 19 ARG cc_start: 0.7716 (ttt-90) cc_final: 0.7175 (mmm-85) REVERT: Y 19 ARG cc_start: 0.7985 (ttt-90) cc_final: 0.7769 (ttt-90) outliers start: 46 outliers final: 36 residues processed: 241 average time/residue: 0.1131 time to fit residues: 39.6084 Evaluate side-chains 240 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 81 LEU Chi-restraints excluded: chain H residue 91 GLU 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 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 21 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 91 GLU Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 91 GLU 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: chunk 135 optimal weight: 3.9990 chunk 62 optimal weight: 30.0000 chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 114 optimal weight: 0.0370 chunk 149 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN E 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.189579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150839 restraints weight = 15153.599| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.81 r_work: 0.3434 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12600 Z= 0.143 Angle : 0.564 5.847 17172 Z= 0.295 Chirality : 0.043 0.138 1872 Planarity : 0.004 0.043 2217 Dihedral : 4.773 39.325 1739 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.57 % Allowed : 16.08 % Favored : 80.34 % 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: -0.33 (0.21), residues: 1554 helix: 1.59 (0.49), residues: 126 sheet: 0.03 (0.21), residues: 591 loop : -0.64 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 97 TYR 0.014 0.001 TYR H 97 PHE 0.016 0.002 PHE F 592 TRP 0.012 0.001 TRP Y 36 HIS 0.002 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (12573) covalent geometry : angle 0.55964 / 0.29 (17112) SS BOND : bond 0.00266 / 0.18 ( 21) SS BOND : angle 1.18603 / 0.80 ( 42) hydrogen bonds : bond 0.04226 / 2.87 ( 397) hydrogen bonds : angle 4.51538 / 3.11 ( 1149) link_BETA1-4 : bond 0.00341 / 0.17 ( 3) link_BETA1-4 : angle 1.99327 / 1.06 ( 9) link_NAG-ASN : bond 0.00035 / 0.02 ( 3) link_NAG-ASN : angle 0.75341 / 0.36 ( 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 248 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6775 (ttt-90) REVERT: H 61 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6672 (m-30) REVERT: D 596 ARG cc_start: 0.8480 (mtt90) cc_final: 0.8239 (mtt90) REVERT: U 51 ILE cc_start: 0.8294 (mm) cc_final: 0.8056 (mt) REVERT: U 109 LYS cc_start: 0.7140 (tppt) cc_final: 0.6820 (tppt) REVERT: C 188 GLN cc_start: 0.6141 (tp40) cc_final: 0.5627 (mm-40) REVERT: C 228 ASN cc_start: 0.8543 (t0) cc_final: 0.8178 (t0) REVERT: E 228 ASN cc_start: 0.8446 (t0) cc_final: 0.8163 (t0) REVERT: P 18 LEU cc_start: 0.7837 (tp) cc_final: 0.7469 (mt) REVERT: P 82 TYR cc_start: 0.7953 (m-80) cc_final: 0.7718 (m-80) outliers start: 46 outliers final: 33 residues processed: 225 average time/residue: 0.1147 time to fit residues: 37.4894 Evaluate side-chains 231 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 B residue 527 ILE Chi-restraints excluded: chain B residue 576 THR 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 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 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 81 LEU Chi-restraints excluded: chain P residue 109 TYR 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: chunk 27 optimal weight: 0.0030 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 ASN C 39 HIS ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.186811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148070 restraints weight = 15167.159| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.71 r_work: 0.3374 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2737 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= 0.212 Angle : 0.627 7.655 17172 Z= 0.326 Chirality : 0.045 0.166 1872 Planarity : 0.005 0.044 2217 Dihedral : 4.864 39.342 1737 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.42 % Allowed : 16.63 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.45 (0.21), residues: 1554 helix: 1.23 (0.48), residues: 126 sheet: -0.03 (0.21), residues: 588 loop : -0.69 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 97 TYR 0.018 0.002 TYR H 97 PHE 0.017 0.002 PHE F 592 TRP 0.013 0.001 TRP Y 36 HIS 0.003 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.21 (12573) covalent geometry : angle 0.62191 / 0.32 (17112) SS BOND : bond 0.00388 / 0.23 ( 21) SS BOND : angle 1.47549 / 0.91 ( 42) hydrogen bonds : bond 0.04773 / 3.27 ( 397) hydrogen bonds : angle 4.60945 / 3.18 ( 1149) link_BETA1-4 : bond 0.00327 / 0.16 ( 3) link_BETA1-4 : angle 2.01818 / 1.07 ( 9) link_NAG-ASN : bond 0.00134 / 0.07 ( 3) link_NAG-ASN : angle 0.86046 / 0.44 ( 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 251 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7170 (ttm170) cc_final: 0.6178 (ttm170) REVERT: H 61 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6703 (m-30) REVERT: H 85 MET cc_start: 0.7194 (ptp) cc_final: 0.6957 (pmm) REVERT: A 228 ASN cc_start: 0.8706 (t0) cc_final: 0.8463 (t0) REVERT: D 596 ARG cc_start: 0.8527 (mtt90) cc_final: 0.8023 (mtt90) REVERT: O 109 LYS cc_start: 0.6832 (tppt) cc_final: 0.6516 (tppt) REVERT: U 51 ILE cc_start: 0.8334 (mm) cc_final: 0.8089 (mt) REVERT: C 188 GLN cc_start: 0.6257 (tp40) cc_final: 0.5744 (mm-40) REVERT: C 228 ASN cc_start: 0.8586 (t0) cc_final: 0.8267 (t0) REVERT: E 120 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7663 (mt-10) REVERT: E 188 GLN cc_start: 0.6224 (tp40) cc_final: 0.5835 (mm-40) REVERT: E 228 ASN cc_start: 0.8500 (t0) cc_final: 0.8232 (t0) REVERT: P 18 LEU cc_start: 0.7784 (tp) cc_final: 0.7521 (mt) REVERT: P 19 ARG cc_start: 0.7766 (ttt-90) cc_final: 0.7419 (tpt-90) REVERT: Y 82 TYR cc_start: 0.7978 (m-80) cc_final: 0.7693 (m-80) outliers start: 44 outliers final: 33 residues processed: 229 average time/residue: 0.1129 time to fit residues: 37.4621 Evaluate side-chains 226 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 61 ASP 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 578 GLU Chi-restraints excluded: chain D residue 505 VAL 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 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 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 7 SER 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 81 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.186166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146935 restraints weight = 15154.292| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.71 r_work: 0.3368 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12600 Z= 0.204 Angle : 0.623 6.657 17172 Z= 0.324 Chirality : 0.044 0.141 1872 Planarity : 0.005 0.054 2217 Dihedral : 4.706 39.325 1733 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.34 % Allowed : 17.33 % Favored : 79.33 % 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: 1.13 (0.48), residues: 126 sheet: 0.30 (0.23), residues: 531 loop : -0.85 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 97 TYR 0.017 0.002 TYR H 97 PHE 0.017 0.002 PHE F 592 TRP 0.012 0.001 TRP Y 36 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.20 (12573) covalent geometry : angle 0.61728 / 0.32 (17112) SS BOND : bond 0.00340 / 0.21 ( 21) SS BOND : angle 1.50652 / 1.00 ( 42) hydrogen bonds : bond 0.04778 / 3.26 ( 397) hydrogen bonds : angle 4.64992 / 3.22 ( 1149) link_BETA1-4 : bond 0.00348 / 0.17 ( 3) link_BETA1-4 : angle 2.01141 / 1.06 ( 9) link_NAG-ASN : bond 0.00104 / 0.05 ( 3) link_NAG-ASN : angle 0.98742 / 0.50 ( 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 242 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 34 TYR cc_start: 0.8630 (m-80) cc_final: 0.8426 (m-80) REVERT: H 19 ARG cc_start: 0.7073 (ttm170) cc_final: 0.6034 (ttm170) REVERT: H 61 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6604 (m-30) REVERT: A 228 ASN cc_start: 0.8706 (t0) cc_final: 0.8406 (t0) REVERT: D 596 ARG cc_start: 0.8533 (mtt90) cc_final: 0.7998 (mtt90) REVERT: U 109 LYS cc_start: 0.7076 (tppt) cc_final: 0.6730 (tppt) REVERT: C 188 GLN cc_start: 0.6259 (tp40) cc_final: 0.5749 (mm-40) REVERT: C 228 ASN cc_start: 0.8579 (t0) cc_final: 0.8306 (t0) REVERT: E 120 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7687 (mt-10) REVERT: E 188 GLN cc_start: 0.6250 (tp40) cc_final: 0.5869 (mm-40) REVERT: E 228 ASN cc_start: 0.8551 (t0) cc_final: 0.8242 (t0) REVERT: P 19 ARG cc_start: 0.7755 (ttt-90) cc_final: 0.7513 (tpt-90) REVERT: Y 82 TYR cc_start: 0.7990 (m-80) cc_final: 0.7677 (m-80) REVERT: Y 84 GLN cc_start: 0.8309 (tp40) cc_final: 0.7750 (mp10) outliers start: 43 outliers final: 35 residues processed: 223 average time/residue: 0.1075 time to fit residues: 35.3924 Evaluate side-chains 228 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 61 ASP 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 A residue 227 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 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 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 7 SER 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 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: chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.187077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148739 restraints weight = 15068.460| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.74 r_work: 0.3396 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12600 Z= 0.156 Angle : 0.605 7.834 17172 Z= 0.314 Chirality : 0.044 0.153 1872 Planarity : 0.004 0.046 2217 Dihedral : 4.479 17.299 1731 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.11 % Allowed : 17.48 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1554 helix: 1.39 (0.49), residues: 126 sheet: -0.02 (0.22), residues: 579 loop : -0.72 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 97 TYR 0.018 0.001 TYR H 62 PHE 0.015 0.002 PHE F 592 TRP 0.011 0.001 TRP Y 36 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (12573) covalent geometry : angle 0.60088 / 0.31 (17112) SS BOND : bond 0.00283 / 0.17 ( 21) SS BOND : angle 1.31553 / 0.88 ( 42) hydrogen bonds : bond 0.04409 / 2.98 ( 397) hydrogen bonds : angle 4.55233 / 3.14 ( 1149) link_BETA1-4 : bond 0.00324 / 0.16 ( 3) link_BETA1-4 : angle 1.99571 / 1.06 ( 9) link_NAG-ASN : bond 0.00038 / 0.02 ( 3) link_NAG-ASN : angle 0.92181 / 0.45 ( 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 242 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: L 52 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.8176 (t80) REVERT: L 100 ASP cc_start: 0.8223 (m-30) cc_final: 0.7944 (m-30) REVERT: H 61 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6502 (m-30) REVERT: H 85 MET cc_start: 0.6990 (ptp) cc_final: 0.6726 (pmm) REVERT: A 228 ASN cc_start: 0.8585 (t0) cc_final: 0.8302 (t0) REVERT: B 596 ARG cc_start: 0.8879 (mtm-85) cc_final: 0.8420 (mtt90) REVERT: D 596 ARG cc_start: 0.8520 (mtt90) cc_final: 0.7897 (mtt90) REVERT: C 188 GLN cc_start: 0.6292 (tp40) cc_final: 0.5806 (mm-40) REVERT: C 228 ASN cc_start: 0.8577 (t0) cc_final: 0.8205 (t0) REVERT: E 120 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7617 (mt-10) REVERT: E 188 GLN cc_start: 0.6100 (tp40) cc_final: 0.5761 (mm-40) REVERT: E 228 ASN cc_start: 0.8482 (t0) cc_final: 0.8267 (t0) REVERT: P 18 LEU cc_start: 0.7842 (tp) cc_final: 0.7489 (tp) REVERT: P 82 TYR cc_start: 0.8083 (m-80) cc_final: 0.7812 (m-80) REVERT: P 84 GLN cc_start: 0.8329 (tp40) cc_final: 0.7831 (mp10) REVERT: Y 82 TYR cc_start: 0.7947 (m-80) cc_final: 0.7629 (m-80) REVERT: Y 84 GLN cc_start: 0.8271 (tp40) cc_final: 0.7768 (mp10) outliers start: 40 outliers final: 36 residues processed: 226 average time/residue: 0.1132 time to fit residues: 37.0128 Evaluate side-chains 241 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 L residue 92 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 61 ASP 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 A residue 227 THR 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 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN 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 175 THR Chi-restraints excluded: chain P residue 7 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.180165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141299 restraints weight = 15436.258| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.50 r_work: 0.3306 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12600 Z= 0.207 Angle : 0.648 7.814 17172 Z= 0.336 Chirality : 0.045 0.175 1872 Planarity : 0.005 0.051 2217 Dihedral : 4.589 17.255 1731 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.34 % Allowed : 17.64 % Favored : 79.02 % 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: -0.53 (0.21), residues: 1554 helix: 1.16 (0.49), residues: 126 sheet: 0.28 (0.23), residues: 519 loop : -0.96 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 97 TYR 0.017 0.002 TYR P 97 PHE 0.018 0.002 PHE F 592 TRP 0.014 0.001 TRP Y 36 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 (12573) covalent geometry : angle 0.64315 / 0.33 (17112) SS BOND : bond 0.00312 / 0.19 ( 21) SS BOND : angle 1.36604 / 0.89 ( 42) hydrogen bonds : bond 0.04818 / 3.28 ( 397) hydrogen bonds : angle 4.65523 / 3.22 ( 1149) link_BETA1-4 : bond 0.00299 / 0.15 ( 3) link_BETA1-4 : angle 2.02478 / 1.07 ( 9) link_NAG-ASN : bond 0.00098 / 0.05 ( 3) link_NAG-ASN : angle 0.95361 / 0.49 ( 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 241 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 34 TYR cc_start: 0.8661 (m-80) cc_final: 0.8440 (m-80) REVERT: H 61 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6566 (m-30) REVERT: H 85 MET cc_start: 0.7128 (ptp) cc_final: 0.6853 (pmm) REVERT: A 228 ASN cc_start: 0.8656 (t0) cc_final: 0.8416 (t0) REVERT: D 596 ARG cc_start: 0.8560 (mtt90) cc_final: 0.7922 (mtt90) REVERT: C 188 GLN cc_start: 0.6403 (tp40) cc_final: 0.5899 (mm-40) REVERT: C 228 ASN cc_start: 0.8594 (t0) cc_final: 0.8287 (t0) REVERT: E 120 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7746 (mt-10) REVERT: E 188 GLN cc_start: 0.6174 (tp40) cc_final: 0.5801 (mm-40) REVERT: E 228 ASN cc_start: 0.8517 (t0) cc_final: 0.8269 (t0) REVERT: P 18 LEU cc_start: 0.7926 (tp) cc_final: 0.7418 (mt) REVERT: P 82 TYR cc_start: 0.8232 (m-80) cc_final: 0.7934 (m-80) REVERT: P 84 GLN cc_start: 0.8279 (tp40) cc_final: 0.7719 (mp10) REVERT: Y 18 LEU cc_start: 0.8340 (tp) cc_final: 0.7306 (mp) REVERT: Y 62 TYR cc_start: 0.7016 (m-10) cc_final: 0.6810 (m-10) REVERT: Y 84 GLN cc_start: 0.8240 (tp40) cc_final: 0.7709 (mp10) outliers start: 43 outliers final: 39 residues processed: 224 average time/residue: 0.1126 time to fit residues: 36.7476 Evaluate side-chains 234 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 61 ASP 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 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 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 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 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 80 THR 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 99 THR 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: chunk 20 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.193339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.152974 restraints weight = 14876.061| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.90 r_work: 0.3385 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12600 Z= 0.140 Angle : 0.602 8.864 17172 Z= 0.314 Chirality : 0.043 0.174 1872 Planarity : 0.004 0.046 2217 Dihedral : 4.448 17.162 1731 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.80 % Allowed : 18.18 % Favored : 79.02 % 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: -0.50 (0.21), residues: 1554 helix: 1.50 (0.49), residues: 126 sheet: -0.02 (0.22), residues: 579 loop : -0.80 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 97 TYR 0.016 0.001 TYR P 82 PHE 0.013 0.001 PHE F 592 TRP 0.011 0.001 TRP Y 36 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (12573) covalent geometry : angle 0.59831 / 0.31 (17112) SS BOND : bond 0.00262 / 0.16 ( 21) SS BOND : angle 1.20621 / 0.80 ( 42) hydrogen bonds : bond 0.04242 / 2.87 ( 397) hydrogen bonds : angle 4.58805 / 3.16 ( 1149) link_BETA1-4 : bond 0.00326 / 0.16 ( 3) link_BETA1-4 : angle 2.00807 / 1.07 ( 9) link_NAG-ASN : bond 0.00080 / 0.04 ( 3) link_NAG-ASN : angle 0.89967 / 0.44 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2782.62 seconds wall clock time: 48 minutes 36.78 seconds (2916.78 seconds total)