Starting phenix.real_space_refine on Wed Jun 11 01:09:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s8d_10118/06_2025/6s8d_10118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8d_10118/06_2025/6s8d_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6s8d_10118/06_2025/6s8d_10118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8d_10118/06_2025/6s8d_10118.map" model { file = "/net/cci-nas-00/data/ceres_data/6s8d_10118/06_2025/6s8d_10118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8d_10118/06_2025/6s8d_10118.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: O, U, D, F, I, J, C, E, P, Y Time building chain proxies: 6.66, per 1000 atoms: 0.54 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: 3.69 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 3.12 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: 6.85 Time building geometry restraints manager: 4.28 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: 6742 17.85 - 35.70: 565 35.70 - 53.56: 115 53.56 - 71.41: 21 71.41 - 89.26: 15 Dihedral angle restraints: 7458 sinusoidal: 2961 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 7455 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: 0.17 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } 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: 49.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.540 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 37.020 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.180 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:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 13.950 88.998 4551 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.26 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (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 TRP 0.011 0.001 TRP D 597 HIS 0.004 0.001 HIS F 516 PHE 0.014 0.002 PHE C 132 TYR 0.021 0.002 TYR P 97 ARG 0.004 0.000 ARG D 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 3) link_NAG-ASN : angle 1.45233 ( 9) link_BETA1-4 : bond 0.06526 ( 3) link_BETA1-4 : angle 29.67574 ( 9) hydrogen bonds : bond 0.15875 ( 397) hydrogen bonds : angle 7.63916 ( 1149) SS BOND : bond 0.02903 ( 21) SS BOND : angle 2.29635 ( 42) covalent geometry : bond 0.00579 (12573) covalent geometry : angle 0.85068 (17112) *********************** 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 : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8253 (m-30) cc_final: 0.8006 (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: 0.2624 time to fit residues: 103.1743 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 : 1.251 ------------------------------------------------------------------------------- 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 131 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 61 ASN B 516 HIS D 516 HIS F 516 HIS O 56 ASN U 56 ASN C 39 HIS C 61 ASN C 188 GLN E 39 HIS E 61 ASN 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 = 0.4247 r_free = 0.4247 target = 0.194004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.159159 restraints weight = 14655.084| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.10 r_work: 0.3553 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12600 Z= 0.144 Angle : 0.642 6.251 17172 Z= 0.337 Chirality : 0.045 0.163 1872 Planarity : 0.005 0.042 2217 Dihedral : 7.740 91.072 1881 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.49 % Allowed : 12.51 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1554 helix: 1.56 (0.47), residues: 126 sheet: 0.11 (0.20), residues: 630 loop : -0.75 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 104 HIS 0.005 0.001 HIS H 101 PHE 0.016 0.002 PHE D 592 TYR 0.012 0.001 TYR Y 62 ARG 0.008 0.001 ARG Y 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 3) link_NAG-ASN : angle 1.70835 ( 9) link_BETA1-4 : bond 0.00142 ( 3) link_BETA1-4 : angle 2.79576 ( 9) hydrogen bonds : bond 0.05325 ( 397) hydrogen bonds : angle 5.39122 ( 1149) SS BOND : bond 0.00322 ( 21) SS BOND : angle 1.47160 ( 42) covalent geometry : bond 0.00324 (12573) covalent geometry : angle 0.63473 (17112) *********************** 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 237 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7097 (ttm170) cc_final: 0.6196 (ttm170) REVERT: B 596 ARG cc_start: 0.8394 (mtt90) cc_final: 0.7439 (mtm-85) REVERT: D 510 LYS cc_start: 0.7352 (mppt) cc_final: 0.7150 (mppt) REVERT: F 545 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7240 (mt-10) REVERT: O 97 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7913 (mtm-85) REVERT: C 228 ASN cc_start: 0.8400 (t0) cc_final: 0.8169 (t0) REVERT: P 3 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7263 (tm-30) REVERT: P 18 LEU cc_start: 0.8027 (tp) cc_final: 0.7633 (mp) REVERT: Y 19 ARG cc_start: 0.7718 (ttt-90) cc_final: 0.7257 (ttt90) outliers start: 32 outliers final: 19 residues processed: 220 average time/residue: 0.3667 time to fit residues: 114.6284 Evaluate side-chains 204 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 99 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 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 14 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 98 optimal weight: 0.0170 chunk 102 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 29 ASN H 3 GLN U 29 ASN C 188 GLN E 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.194005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.158817 restraints weight = 14800.549| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.10 r_work: 0.3536 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1822 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= 0.134 Angle : 0.578 6.037 17172 Z= 0.302 Chirality : 0.043 0.160 1872 Planarity : 0.004 0.050 2217 Dihedral : 6.211 38.740 1868 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.19 % Allowed : 13.91 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1554 helix: 1.59 (0.49), residues: 126 sheet: 0.07 (0.20), residues: 645 loop : -0.65 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS C 139 PHE 0.020 0.002 PHE H 29 TYR 0.012 0.001 TYR H 97 ARG 0.007 0.000 ARG P 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 3) link_NAG-ASN : angle 1.07856 ( 9) link_BETA1-4 : bond 0.00310 ( 3) link_BETA1-4 : angle 2.46549 ( 9) hydrogen bonds : bond 0.04620 ( 397) hydrogen bonds : angle 4.91110 ( 1149) SS BOND : bond 0.00243 ( 21) SS BOND : angle 1.08608 ( 42) covalent geometry : bond 0.00314 (12573) covalent geometry : angle 0.57278 (17112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7092 (ttm170) cc_final: 0.6155 (ttm170) REVERT: C 228 ASN cc_start: 0.8480 (t0) cc_final: 0.8249 (t0) REVERT: E 228 ASN cc_start: 0.8525 (t0) cc_final: 0.8229 (t0) REVERT: P 3 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7445 (tm-30) outliers start: 41 outliers final: 24 residues processed: 223 average time/residue: 0.3721 time to fit residues: 119.4727 Evaluate side-chains 211 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain 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 29 ASN Chi-restraints excluded: chain U residue 99 SER 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 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 116 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 29 ASN H 3 GLN A 188 GLN D 516 HIS U 29 ASN C 188 GLN E 188 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.197415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156545 restraints weight = 14845.151| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.77 r_work: 0.3484 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2142 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= 0.124 Angle : 0.570 6.556 17172 Z= 0.298 Chirality : 0.043 0.153 1872 Planarity : 0.004 0.040 2217 Dihedral : 5.747 38.916 1867 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.19 % Allowed : 13.99 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1554 helix: 1.70 (0.49), residues: 126 sheet: 0.18 (0.22), residues: 585 loop : -0.62 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.002 0.001 HIS A 154 PHE 0.016 0.001 PHE D 592 TYR 0.012 0.001 TYR H 97 ARG 0.006 0.000 ARG O 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 3) link_NAG-ASN : angle 1.04424 ( 9) link_BETA1-4 : bond 0.00402 ( 3) link_BETA1-4 : angle 2.30552 ( 9) hydrogen bonds : bond 0.04201 ( 397) hydrogen bonds : angle 4.69020 ( 1149) SS BOND : bond 0.00260 ( 21) SS BOND : angle 1.27793 ( 42) covalent geometry : bond 0.00286 (12573) covalent geometry : angle 0.56476 (17112) *********************** 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 238 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7050 (ttm170) cc_final: 0.6104 (ttm170) REVERT: H 61 ASP cc_start: 0.6965 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: U 29 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8335 (p0) REVERT: C 228 ASN cc_start: 0.8591 (t0) cc_final: 0.8280 (t0) REVERT: E 228 ASN cc_start: 0.8556 (t0) cc_final: 0.8350 (t0) REVERT: P 3 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7441 (tm-30) REVERT: P 18 LEU cc_start: 0.7964 (tp) cc_final: 0.7671 (mt) outliers start: 41 outliers final: 29 residues processed: 218 average time/residue: 0.2567 time to fit residues: 79.6041 Evaluate side-chains 216 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 61 ASP 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 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 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 C residue 231 GLU 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 81 LEU Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.0050 chunk 40 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN 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 = 0.4203 r_free = 0.4203 target = 0.191542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153621 restraints weight = 15082.711| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.70 r_work: 0.3461 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12600 Z= 0.131 Angle : 0.569 7.041 17172 Z= 0.297 Chirality : 0.043 0.144 1872 Planarity : 0.004 0.044 2217 Dihedral : 5.478 39.320 1865 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.26 % Allowed : 14.84 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1554 helix: 1.74 (0.48), residues: 126 sheet: 0.15 (0.22), residues: 585 loop : -0.56 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.002 0.001 HIS D 516 PHE 0.016 0.002 PHE B 592 TYR 0.013 0.001 TYR H 97 ARG 0.007 0.000 ARG U 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 3) link_NAG-ASN : angle 1.04339 ( 9) link_BETA1-4 : bond 0.00376 ( 3) link_BETA1-4 : angle 2.26971 ( 9) hydrogen bonds : bond 0.04128 ( 397) hydrogen bonds : angle 4.54476 ( 1149) SS BOND : bond 0.00227 ( 21) SS BOND : angle 1.01260 ( 42) covalent geometry : bond 0.00310 (12573) covalent geometry : angle 0.56512 (17112) *********************** 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 246 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 510 LYS cc_start: 0.7359 (mppt) cc_final: 0.7153 (tmtt) REVERT: O 109 LYS cc_start: 0.6866 (tppt) cc_final: 0.6594 (tppt) REVERT: U 29 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8214 (p0) REVERT: C 228 ASN cc_start: 0.8524 (t0) cc_final: 0.8210 (t0) REVERT: P 18 LEU cc_start: 0.7824 (tp) cc_final: 0.7576 (mt) REVERT: P 19 ARG cc_start: 0.7699 (ttt-90) cc_final: 0.7254 (mmm-85) REVERT: P 61 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6436 (m-30) REVERT: Y 84 GLN cc_start: 0.8282 (tp40) cc_final: 0.8067 (mm110) REVERT: Y 93 THR cc_start: 0.8720 (p) cc_final: 0.8489 (p) outliers start: 42 outliers final: 30 residues processed: 226 average time/residue: 0.2675 time to fit residues: 87.2073 Evaluate side-chains 228 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 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 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 U residue 4 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 96 ILE Chi-restraints excluded: chain C residue 52 VAL 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 61 ASP Chi-restraints excluded: chain P residue 91 GLU Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN A 188 GLN U 29 ASN E 39 HIS E 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.186450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.149420 restraints weight = 15349.695| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.63 r_work: 0.3399 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12600 Z= 0.243 Angle : 0.653 6.034 17172 Z= 0.342 Chirality : 0.046 0.165 1872 Planarity : 0.005 0.048 2217 Dihedral : 5.681 39.550 1865 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.57 % Allowed : 15.70 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1554 helix: 1.21 (0.48), residues: 126 sheet: 0.37 (0.22), residues: 549 loop : -0.82 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 36 HIS 0.004 0.001 HIS D 516 PHE 0.021 0.003 PHE B 592 TYR 0.020 0.002 TYR H 97 ARG 0.005 0.001 ARG P 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 3) link_NAG-ASN : angle 1.02058 ( 9) link_BETA1-4 : bond 0.00269 ( 3) link_BETA1-4 : angle 2.28015 ( 9) hydrogen bonds : bond 0.05093 ( 397) hydrogen bonds : angle 4.66325 ( 1149) SS BOND : bond 0.00310 ( 21) SS BOND : angle 1.29569 ( 42) covalent geometry : bond 0.00603 (12573) covalent geometry : angle 0.64869 (17112) *********************** 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 252 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASN cc_start: 0.8570 (t0) cc_final: 0.8296 (t0) REVERT: U 29 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8418 (p0) REVERT: U 51 ILE cc_start: 0.8371 (mm) cc_final: 0.8150 (mt) REVERT: U 109 LYS cc_start: 0.7185 (tppt) cc_final: 0.6821 (tppt) REVERT: C 188 GLN cc_start: 0.6033 (tp40) cc_final: 0.5648 (mm-40) REVERT: C 228 ASN cc_start: 0.8539 (t0) cc_final: 0.8195 (t0) REVERT: P 18 LEU cc_start: 0.7794 (tp) cc_final: 0.7500 (mt) outliers start: 46 outliers final: 36 residues processed: 233 average time/residue: 0.3150 time to fit residues: 106.9579 Evaluate side-chains 225 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 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 C residue 227 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 99 THR Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 0.4980 chunk 118 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 29 ASN E 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.190707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152325 restraints weight = 15136.300| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.73 r_work: 0.3437 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2700 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= 0.111 Angle : 0.565 6.499 17172 Z= 0.296 Chirality : 0.043 0.169 1872 Planarity : 0.004 0.045 2217 Dihedral : 5.256 39.056 1863 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.72 % Allowed : 17.09 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1554 helix: 1.67 (0.48), residues: 126 sheet: 0.40 (0.22), residues: 549 loop : -0.78 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 36 HIS 0.001 0.000 HIS D 516 PHE 0.015 0.001 PHE H 29 TYR 0.011 0.001 TYR P 110 ARG 0.006 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 3) link_NAG-ASN : angle 1.05668 ( 9) link_BETA1-4 : bond 0.00382 ( 3) link_BETA1-4 : angle 2.35138 ( 9) hydrogen bonds : bond 0.03959 ( 397) hydrogen bonds : angle 4.51112 ( 1149) SS BOND : bond 0.00242 ( 21) SS BOND : angle 1.07457 ( 42) covalent geometry : bond 0.00258 (12573) covalent geometry : angle 0.56053 (17112) *********************** 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 230 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8267 (m-30) cc_final: 0.8063 (m-30) REVERT: H 85 MET cc_start: 0.6902 (ptp) cc_final: 0.6379 (ptp) REVERT: A 172 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8344 (ttm170) REVERT: F 591 ASP cc_start: 0.8481 (m-30) cc_final: 0.8132 (m-30) REVERT: O 109 LYS cc_start: 0.6867 (tppt) cc_final: 0.6639 (tppt) REVERT: U 29 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8263 (p0) REVERT: C 188 GLN cc_start: 0.6044 (tp40) cc_final: 0.5655 (mm-40) REVERT: C 228 ASN cc_start: 0.8532 (t0) cc_final: 0.8194 (t0) REVERT: E 106 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8249 (mm-30) REVERT: E 188 GLN cc_start: 0.6202 (tp40) cc_final: 0.5772 (mm-40) REVERT: P 110 TYR cc_start: 0.8518 (m-80) cc_final: 0.8251 (m-10) outliers start: 35 outliers final: 27 residues processed: 216 average time/residue: 0.2398 time to fit residues: 74.3927 Evaluate side-chains 211 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain F residue 505 VAL 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 175 THR Chi-restraints excluded: chain E residue 52 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 21 SER Chi-restraints excluded: chain Y residue 81 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 33 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.185592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147908 restraints weight = 15328.105| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.80 r_work: 0.3381 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12600 Z= 0.243 Angle : 0.662 7.003 17172 Z= 0.345 Chirality : 0.046 0.146 1872 Planarity : 0.005 0.055 2217 Dihedral : 5.333 39.387 1859 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.26 % Allowed : 16.86 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1554 helix: 1.15 (0.48), residues: 126 sheet: 0.37 (0.23), residues: 510 loop : -0.87 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 36 HIS 0.004 0.001 HIS D 516 PHE 0.020 0.002 PHE B 592 TYR 0.019 0.002 TYR H 97 ARG 0.006 0.001 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 3) link_NAG-ASN : angle 1.08198 ( 9) link_BETA1-4 : bond 0.00298 ( 3) link_BETA1-4 : angle 2.29275 ( 9) hydrogen bonds : bond 0.04995 ( 397) hydrogen bonds : angle 4.59968 ( 1149) SS BOND : bond 0.00415 ( 21) SS BOND : angle 1.50093 ( 42) covalent geometry : bond 0.00605 (12573) covalent geometry : angle 0.65649 (17112) *********************** 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 236 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 85 MET cc_start: 0.7046 (ptp) cc_final: 0.6518 (ptp) REVERT: A 228 ASN cc_start: 0.8555 (t0) cc_final: 0.8315 (t0) REVERT: U 29 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8366 (p0) REVERT: U 109 LYS cc_start: 0.7052 (tppt) cc_final: 0.6660 (tppt) REVERT: C 188 GLN cc_start: 0.6125 (tp40) cc_final: 0.5716 (mm-40) REVERT: C 228 ASN cc_start: 0.8531 (t0) cc_final: 0.8229 (t0) REVERT: E 188 GLN cc_start: 0.6148 (tp40) cc_final: 0.5774 (mm-40) REVERT: P 18 LEU cc_start: 0.8061 (tp) cc_final: 0.7546 (mt) REVERT: Y 82 TYR cc_start: 0.7952 (m-80) cc_final: 0.7677 (m-80) outliers start: 42 outliers final: 29 residues processed: 218 average time/residue: 0.2567 time to fit residues: 81.5817 Evaluate side-chains 213 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 80 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain D residue 505 VAL 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 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 106 GLU 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 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.188667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151080 restraints weight = 15140.059| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.81 r_work: 0.3430 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12600 Z= 0.141 Angle : 0.610 8.846 17172 Z= 0.318 Chirality : 0.043 0.156 1872 Planarity : 0.004 0.047 2217 Dihedral : 5.038 27.076 1857 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.56 % Allowed : 17.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1554 helix: 1.47 (0.48), residues: 126 sheet: 0.26 (0.22), residues: 546 loop : -0.84 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 36 HIS 0.002 0.001 HIS D 516 PHE 0.020 0.002 PHE H 29 TYR 0.013 0.001 TYR H 97 ARG 0.007 0.000 ARG P 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 3) link_NAG-ASN : angle 1.11005 ( 9) link_BETA1-4 : bond 0.00365 ( 3) link_BETA1-4 : angle 2.29836 ( 9) hydrogen bonds : bond 0.04257 ( 397) hydrogen bonds : angle 4.49594 ( 1149) SS BOND : bond 0.00289 ( 21) SS BOND : angle 1.49948 ( 42) covalent geometry : bond 0.00340 (12573) covalent geometry : angle 0.60393 (17112) *********************** 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 234 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8278 (m-30) cc_final: 0.8066 (m-30) REVERT: H 61 ASP cc_start: 0.6840 (OUTLIER) cc_final: 0.6470 (m-30) REVERT: H 85 MET cc_start: 0.6978 (ptp) cc_final: 0.6435 (ptp) REVERT: A 120 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7430 (mt-10) REVERT: A 228 ASN cc_start: 0.8504 (t0) cc_final: 0.8227 (t0) REVERT: U 29 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8079 (p0) REVERT: U 109 LYS cc_start: 0.7019 (tppt) cc_final: 0.6720 (tppt) REVERT: C 188 GLN cc_start: 0.6076 (tp40) cc_final: 0.5694 (mm-40) REVERT: C 228 ASN cc_start: 0.8548 (t0) cc_final: 0.8263 (t0) REVERT: E 188 GLN cc_start: 0.6133 (tp40) cc_final: 0.5790 (mm-40) REVERT: P 18 LEU cc_start: 0.7913 (tp) cc_final: 0.7052 (mt) REVERT: P 19 ARG cc_start: 0.7806 (tpt-90) cc_final: 0.7595 (tpt-90) REVERT: P 82 TYR cc_start: 0.7798 (m-80) cc_final: 0.7523 (m-80) REVERT: Y 18 LEU cc_start: 0.7765 (tp) cc_final: 0.7335 (tp) REVERT: Y 82 TYR cc_start: 0.7888 (m-80) cc_final: 0.7584 (m-80) outliers start: 33 outliers final: 26 residues processed: 221 average time/residue: 0.2457 time to fit residues: 77.4040 Evaluate side-chains 226 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 D residue 505 VAL Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 62 optimal weight: 50.0000 chunk 120 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.189216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.150701 restraints weight = 15050.901| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.94 r_work: 0.3411 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12600 Z= 0.142 Angle : 0.613 7.576 17172 Z= 0.320 Chirality : 0.043 0.159 1872 Planarity : 0.004 0.048 2217 Dihedral : 4.967 26.647 1857 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.41 % Allowed : 17.87 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1554 helix: 1.51 (0.48), residues: 126 sheet: 0.34 (0.22), residues: 540 loop : -0.80 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 36 HIS 0.002 0.001 HIS D 516 PHE 0.018 0.002 PHE B 592 TYR 0.014 0.001 TYR H 97 ARG 0.008 0.000 ARG P 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 3) link_NAG-ASN : angle 1.17449 ( 9) link_BETA1-4 : bond 0.00334 ( 3) link_BETA1-4 : angle 2.27632 ( 9) hydrogen bonds : bond 0.04189 ( 397) hydrogen bonds : angle 4.46800 ( 1149) SS BOND : bond 0.00292 ( 21) SS BOND : angle 1.36260 ( 42) covalent geometry : bond 0.00344 (12573) covalent geometry : angle 0.60753 (17112) ********************** 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 230 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8301 (m-30) cc_final: 0.8094 (m-30) REVERT: H 19 ARG cc_start: 0.7277 (ttt-90) cc_final: 0.7056 (tpt-90) REVERT: H 61 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6479 (m-30) REVERT: H 85 MET cc_start: 0.6987 (ptp) cc_final: 0.6457 (ptp) REVERT: A 228 ASN cc_start: 0.8515 (t0) cc_final: 0.8227 (t0) REVERT: C 188 GLN cc_start: 0.6070 (tp40) cc_final: 0.5714 (mm-40) REVERT: C 228 ASN cc_start: 0.8553 (t0) cc_final: 0.8221 (t0) REVERT: E 188 GLN cc_start: 0.6156 (tp40) cc_final: 0.5815 (mm-40) REVERT: Y 82 TYR cc_start: 0.7880 (m-80) cc_final: 0.7579 (m-80) REVERT: Y 93 THR cc_start: 0.8808 (p) cc_final: 0.8598 (p) outliers start: 31 outliers final: 29 residues processed: 217 average time/residue: 0.2480 time to fit residues: 77.8047 Evaluate side-chains 224 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 80 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 540 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain 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 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 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 108 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 107 optimal weight: 0.0980 chunk 155 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.191234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153621 restraints weight = 15205.490| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.72 r_work: 0.3456 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12600 Z= 0.115 Angle : 0.607 7.994 17172 Z= 0.314 Chirality : 0.043 0.171 1872 Planarity : 0.004 0.039 2217 Dihedral : 4.773 25.720 1857 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.10 % Allowed : 18.26 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1554 helix: 1.74 (0.48), residues: 126 sheet: 0.05 (0.22), residues: 576 loop : -0.63 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 36 HIS 0.001 0.000 HIS D 516 PHE 0.015 0.001 PHE Y 29 TYR 0.014 0.001 TYR Y 82 ARG 0.005 0.000 ARG P 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 1.25356 ( 9) link_BETA1-4 : bond 0.00377 ( 3) link_BETA1-4 : angle 2.27888 ( 9) hydrogen bonds : bond 0.03791 ( 397) hydrogen bonds : angle 4.47180 ( 1149) SS BOND : bond 0.00261 ( 21) SS BOND : angle 1.23180 ( 42) covalent geometry : bond 0.00266 (12573) covalent geometry : angle 0.60219 (17112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6212.26 seconds wall clock time: 110 minutes 44.61 seconds (6644.61 seconds total)