Starting phenix.real_space_refine on Wed Mar 4 08:40:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s8d_10118/03_2026/6s8d_10118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8d_10118/03_2026/6s8d_10118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6s8d_10118/03_2026/6s8d_10118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8d_10118/03_2026/6s8d_10118.map" model { file = "/net/cci-nas-00/data/ceres_data/6s8d_10118/03_2026/6s8d_10118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8d_10118/03_2026/6s8d_10118.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 7782 2.51 5 N 2091 2.21 5 O 2343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12267 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: O, U, P, Y, C, E, D, F, I, J Time building chain proxies: 2.07, per 1000 atoms: 0.17 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: 0.94 Conformation dependent library (CDL) restraints added in 508.4 milliseconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2844 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 33 sheets defined 12.7% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.871A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.779A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 4.019A pdb=" N ILE B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.680A pdb=" N GLY B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.705A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 4.018A pdb=" N ILE D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.680A pdb=" N GLY D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.705A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 4.019A pdb=" N ILE F 542 " --> pdb=" O ALA F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.679A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.704A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.871A pdb=" N GLU O 86 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 86 removed outlier: 3.872A pdb=" N GLU U 86 " --> pdb=" O ALA U 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.779A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.779A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.480A pdb=" N TRP L 38 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS L 48 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR H 100 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 45 removed outlier: 7.133A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 42 through 45 removed outlier: 7.133A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.453A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AB4, first strand: chain 'D' and resid 580 through 581 removed outlier: 7.132A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 580 through 581 Processing sheet with id=AB6, first strand: chain 'F' and resid 544 through 548 Processing sheet with id=AB7, first strand: chain 'F' and resid 580 through 581 removed outlier: 7.133A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.480A pdb=" N TRP O 38 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS O 48 " --> pdb=" O GLN O 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'O' and resid 18 through 24 Processing sheet with id=AC3, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.479A pdb=" N TRP U 38 " --> pdb=" O ILE U 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS U 48 " --> pdb=" O GLN U 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 10 through 12 Processing sheet with id=AC5, first strand: chain 'U' and resid 18 through 24 Processing sheet with id=AC6, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC7, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.452A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AC9, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.452A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU E 112 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 136 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE E 218 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL E 138 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR E 220 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS E 140 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA E 222 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER E 142 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'P' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR P 100 " --> pdb=" O TYR P 113 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'Y' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR Y 100 " --> pdb=" O TYR Y 113 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.29 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: 0.03 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.950 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- 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 : 10.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.25 % Favored : 95.56 % Rotamer: Outliers : 2.56 % Allowed : 4.74 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.20), residues: 1554 helix: 0.45 (0.43), residues: 126 sheet: -0.17 (0.20), residues: 624 loop : -1.03 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 559 TYR 0.021 0.002 TYR P 97 PHE 0.014 0.002 PHE C 132 TRP 0.011 0.001 TRP D 597 HIS 0.004 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00579 (12573) covalent geometry : angle 0.85068 (17112) SS BOND : bond 0.02903 ( 21) SS BOND : angle 2.29635 ( 42) hydrogen bonds : bond 0.15875 ( 397) hydrogen bonds : angle 7.63916 ( 1149) link_BETA1-4 : bond 0.06526 ( 3) link_BETA1-4 : angle 29.67574 ( 9) link_NAG-ASN : bond 0.00458 ( 3) link_NAG-ASN : angle 1.45233 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8253 (m-30) cc_final: 0.8007 (m-30) REVERT: P 3 GLN cc_start: 0.7395 (tm-30) cc_final: 0.6999 (tm-30) outliers start: 33 outliers final: 12 residues processed: 282 average time/residue: 0.1197 time to fit residues: 47.5024 Evaluate side-chains 202 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain E residue 229 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 ASN A 39 HIS A 61 ASN B 516 HIS D 516 HIS O 56 ASN U 56 ASN C 39 HIS C 61 ASN E 39 HIS E 61 ASN E 188 GLN P 35 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.192915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157042 restraints weight = 14781.088| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.55 r_work: 0.3462 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12600 Z= 0.173 Angle : 0.655 6.272 17172 Z= 0.344 Chirality : 0.046 0.172 1872 Planarity : 0.005 0.042 2217 Dihedral : 7.790 91.038 1881 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.87 % Allowed : 12.28 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1554 helix: 1.38 (0.47), residues: 126 sheet: 0.10 (0.20), residues: 636 loop : -0.81 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 172 TYR 0.014 0.001 TYR Y 62 PHE 0.018 0.002 PHE D 592 TRP 0.007 0.001 TRP H 36 HIS 0.004 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00403 (12573) covalent geometry : angle 0.64745 (17112) SS BOND : bond 0.00394 ( 21) SS BOND : angle 1.59795 ( 42) hydrogen bonds : bond 0.05428 ( 397) hydrogen bonds : angle 5.39128 ( 1149) link_BETA1-4 : bond 0.00594 ( 3) link_BETA1-4 : angle 2.52212 ( 9) link_NAG-ASN : bond 0.00422 ( 3) link_NAG-ASN : angle 1.89265 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 ASP cc_start: 0.8354 (m-30) cc_final: 0.8123 (m-30) REVERT: H 19 ARG cc_start: 0.7152 (ttm170) cc_final: 0.6211 (ttm170) REVERT: H 69 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.7000 (mtp180) REVERT: D 510 LYS cc_start: 0.7363 (mppt) cc_final: 0.7122 (mppt) REVERT: D 596 ARG cc_start: 0.8531 (mtt90) cc_final: 0.8290 (mtt90) REVERT: F 545 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7316 (mt-10) REVERT: O 97 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.7966 (mtm-85) REVERT: C 228 ASN cc_start: 0.8480 (t0) cc_final: 0.8236 (t0) REVERT: P 3 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7297 (tm-30) REVERT: P 18 LEU cc_start: 0.8081 (tp) cc_final: 0.7658 (mp) REVERT: Y 19 ARG cc_start: 0.7757 (ttt-90) cc_final: 0.7293 (ttt90) outliers start: 37 outliers final: 22 residues processed: 228 average time/residue: 0.1208 time to fit residues: 38.6618 Evaluate side-chains 212 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 134 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 150 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 29 ASN U 29 ASN C 188 GLN E 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.194430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158730 restraints weight = 14801.410| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.60 r_work: 0.3494 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12600 Z= 0.120 Angle : 0.580 6.256 17172 Z= 0.302 Chirality : 0.043 0.164 1872 Planarity : 0.004 0.046 2217 Dihedral : 6.169 39.630 1868 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.80 % Allowed : 13.99 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.21), residues: 1554 helix: 1.65 (0.49), residues: 126 sheet: 0.12 (0.21), residues: 615 loop : -0.67 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 19 TYR 0.011 0.001 TYR H 97 PHE 0.020 0.001 PHE H 29 TRP 0.007 0.001 TRP H 36 HIS 0.003 0.001 HIS P 101 Details of bonding type rmsd covalent geometry : bond 0.00268 (12573) covalent geometry : angle 0.57400 (17112) SS BOND : bond 0.00337 ( 21) SS BOND : angle 1.27460 ( 42) hydrogen bonds : bond 0.04408 ( 397) hydrogen bonds : angle 4.87491 ( 1149) link_BETA1-4 : bond 0.00490 ( 3) link_BETA1-4 : angle 2.43829 ( 9) link_NAG-ASN : bond 0.00304 ( 3) link_NAG-ASN : angle 1.09968 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7077 (ttm170) cc_final: 0.6137 (ttm170) REVERT: D 596 ARG cc_start: 0.8522 (mtt90) cc_final: 0.8226 (mtt90) REVERT: C 228 ASN cc_start: 0.8533 (t0) cc_final: 0.8273 (t0) REVERT: P 3 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7445 (tm-30) REVERT: P 110 TYR cc_start: 0.8431 (m-80) cc_final: 0.8203 (m-10) outliers start: 36 outliers final: 25 residues processed: 225 average time/residue: 0.1153 time to fit residues: 36.8323 Evaluate side-chains 212 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 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 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 U 29 ASN C 188 GLN E 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.190765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156087 restraints weight = 14711.202| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.32 r_work: 0.3490 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12600 Z= 0.172 Angle : 0.600 6.530 17172 Z= 0.314 Chirality : 0.044 0.145 1872 Planarity : 0.004 0.041 2217 Dihedral : 5.925 38.912 1865 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.42 % Allowed : 14.92 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1554 helix: 1.49 (0.49), residues: 126 sheet: 0.14 (0.22), residues: 585 loop : -0.70 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 19 TYR 0.015 0.001 TYR H 97 PHE 0.018 0.002 PHE B 592 TRP 0.013 0.001 TRP H 36 HIS 0.003 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00419 (12573) covalent geometry : angle 0.59524 (17112) SS BOND : bond 0.00365 ( 21) SS BOND : angle 1.27544 ( 42) hydrogen bonds : bond 0.04618 ( 397) hydrogen bonds : angle 4.78296 ( 1149) link_BETA1-4 : bond 0.00320 ( 3) link_BETA1-4 : angle 2.29823 ( 9) link_NAG-ASN : bond 0.00099 ( 3) link_NAG-ASN : angle 1.06361 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7096 (ttm170) cc_final: 0.6122 (ttm170) REVERT: H 61 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6748 (m-30) REVERT: D 596 ARG cc_start: 0.8511 (mtt90) cc_final: 0.8175 (mtt90) REVERT: O 69 LYS cc_start: 0.8369 (tttm) cc_final: 0.8073 (tttp) REVERT: U 29 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8437 (p0) REVERT: C 228 ASN cc_start: 0.8540 (t0) cc_final: 0.8231 (t0) REVERT: P 18 LEU cc_start: 0.7953 (tp) cc_final: 0.7672 (mt) REVERT: Y 93 THR cc_start: 0.8619 (p) cc_final: 0.8415 (p) outliers start: 44 outliers final: 30 residues processed: 224 average time/residue: 0.1085 time to fit residues: 34.8918 Evaluate side-chains 231 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain 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 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.191483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155507 restraints weight = 14786.763| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.46 r_work: 0.3486 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12600 Z= 0.142 Angle : 0.577 6.810 17172 Z= 0.302 Chirality : 0.043 0.145 1872 Planarity : 0.004 0.042 2217 Dihedral : 5.606 39.064 1865 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.34 % Allowed : 15.54 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1554 helix: 1.54 (0.49), residues: 126 sheet: 0.08 (0.21), residues: 585 loop : -0.61 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 97 TYR 0.014 0.001 TYR H 97 PHE 0.015 0.002 PHE F 592 TRP 0.010 0.001 TRP H 36 HIS 0.002 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00340 (12573) covalent geometry : angle 0.57268 (17112) SS BOND : bond 0.00294 ( 21) SS BOND : angle 1.13075 ( 42) hydrogen bonds : bond 0.04302 ( 397) hydrogen bonds : angle 4.65334 ( 1149) link_BETA1-4 : bond 0.00385 ( 3) link_BETA1-4 : angle 2.28509 ( 9) link_NAG-ASN : bond 0.00126 ( 3) link_NAG-ASN : angle 1.02178 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7074 (ttm170) cc_final: 0.6144 (ttm170) REVERT: H 61 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6655 (m-30) REVERT: A 120 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7554 (tp30) REVERT: A 228 ASN cc_start: 0.8518 (t0) cc_final: 0.8264 (t0) REVERT: D 596 ARG cc_start: 0.8527 (mtt90) cc_final: 0.8286 (mtt90) REVERT: U 29 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8382 (p0) REVERT: C 228 ASN cc_start: 0.8510 (t0) cc_final: 0.8205 (t0) REVERT: E 120 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7519 (mt-10) REVERT: E 172 ARG cc_start: 0.8639 (ttm170) cc_final: 0.8382 (ttp-170) REVERT: P 18 LEU cc_start: 0.7861 (tp) cc_final: 0.7622 (mt) REVERT: P 19 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7486 (mmm160) REVERT: P 84 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7814 (mm-40) outliers start: 43 outliers final: 32 residues processed: 229 average time/residue: 0.1109 time to fit residues: 36.5695 Evaluate side-chains 235 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 91 GLU 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 527 ILE 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 545 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 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 21 SER Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 135 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 114 optimal weight: 0.0270 chunk 149 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 151 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- 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 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 = 0.4258 r_free = 0.4258 target = 0.196651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.157002 restraints weight = 15132.524| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.70 r_work: 0.3429 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2548 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= 0.132 Angle : 0.562 5.799 17172 Z= 0.293 Chirality : 0.043 0.140 1872 Planarity : 0.004 0.043 2217 Dihedral : 5.366 39.356 1865 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.89 % Allowed : 15.54 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.21), residues: 1554 helix: 1.62 (0.49), residues: 126 sheet: 0.10 (0.21), residues: 585 loop : -0.58 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 97 TYR 0.014 0.001 TYR H 97 PHE 0.016 0.001 PHE F 592 TRP 0.009 0.001 TRP H 36 HIS 0.002 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00314 (12573) covalent geometry : angle 0.55718 (17112) SS BOND : bond 0.00295 ( 21) SS BOND : angle 1.18120 ( 42) hydrogen bonds : bond 0.04131 ( 397) hydrogen bonds : angle 4.52722 ( 1149) link_BETA1-4 : bond 0.00416 ( 3) link_BETA1-4 : angle 2.29696 ( 9) link_NAG-ASN : bond 0.00106 ( 3) link_NAG-ASN : angle 1.01306 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8237 (m-30) cc_final: 0.7941 (m-30) REVERT: H 19 ARG cc_start: 0.7075 (ttm170) cc_final: 0.6128 (ttm170) REVERT: A 120 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7655 (tp30) REVERT: A 228 ASN cc_start: 0.8570 (t0) cc_final: 0.8344 (t0) REVERT: D 596 ARG cc_start: 0.8499 (mtt90) cc_final: 0.8287 (mtt90) REVERT: U 29 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8246 (p0) REVERT: U 109 LYS cc_start: 0.7180 (tppt) cc_final: 0.6812 (tppt) REVERT: C 228 ASN cc_start: 0.8531 (t0) cc_final: 0.8208 (t0) REVERT: E 120 GLU cc_start: 0.8088 (mt-10) cc_final: 0.6970 (mt-10) REVERT: E 172 ARG cc_start: 0.8714 (ttm170) cc_final: 0.8368 (ttm170) REVERT: P 18 LEU cc_start: 0.7816 (tp) cc_final: 0.7515 (mt) REVERT: P 61 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6344 (m-30) outliers start: 50 outliers final: 37 residues processed: 240 average time/residue: 0.1156 time to fit residues: 39.8730 Evaluate side-chains 241 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 48 VAL 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 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 545 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 U residue 96 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 91 GLU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 0.0370 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 29 ASN C 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.189770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.151445 restraints weight = 15172.466| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.71 r_work: 0.3431 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12600 Z= 0.142 Angle : 0.576 7.606 17172 Z= 0.299 Chirality : 0.043 0.139 1872 Planarity : 0.004 0.051 2217 Dihedral : 5.257 39.373 1863 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.50 % Allowed : 16.16 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.21), residues: 1554 helix: 1.57 (0.48), residues: 126 sheet: 0.09 (0.22), residues: 585 loop : -0.59 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 97 TYR 0.014 0.001 TYR H 97 PHE 0.021 0.002 PHE P 29 TRP 0.012 0.001 TRP Y 36 HIS 0.002 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00344 (12573) covalent geometry : angle 0.57015 (17112) SS BOND : bond 0.00490 ( 21) SS BOND : angle 1.39622 ( 42) hydrogen bonds : bond 0.04161 ( 397) hydrogen bonds : angle 4.47007 ( 1149) link_BETA1-4 : bond 0.00421 ( 3) link_BETA1-4 : angle 2.28330 ( 9) link_NAG-ASN : bond 0.00088 ( 3) link_NAG-ASN : angle 1.03427 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8199 (m-30) cc_final: 0.7942 (m-30) REVERT: L 109 LYS cc_start: 0.6945 (tppt) cc_final: 0.6720 (tppt) REVERT: H 19 ARG cc_start: 0.7147 (ttm170) cc_final: 0.6156 (ttm170) REVERT: H 61 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6733 (m-30) REVERT: H 85 MET cc_start: 0.7014 (ptp) cc_final: 0.6577 (ptp) REVERT: D 596 ARG cc_start: 0.8498 (mtt90) cc_final: 0.8272 (mtt90) REVERT: U 51 ILE cc_start: 0.8329 (mm) cc_final: 0.8088 (mt) REVERT: C 188 GLN cc_start: 0.5980 (tp40) cc_final: 0.5590 (mm-40) REVERT: C 228 ASN cc_start: 0.8538 (t0) cc_final: 0.8231 (t0) REVERT: E 228 ASN cc_start: 0.8435 (t0) cc_final: 0.8218 (t0) REVERT: P 18 LEU cc_start: 0.7789 (tp) cc_final: 0.7582 (mt) REVERT: P 61 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.6323 (m-30) outliers start: 45 outliers final: 37 residues processed: 234 average time/residue: 0.1176 time to fit residues: 39.6910 Evaluate side-chains 237 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 61 ASP 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 545 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 149 optimal weight: 0.4980 chunk 81 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 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 = 0.4174 r_free = 0.4174 target = 0.188452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.151413 restraints weight = 15181.220| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.63 r_work: 0.3424 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12600 Z= 0.165 Angle : 0.596 6.861 17172 Z= 0.310 Chirality : 0.044 0.165 1872 Planarity : 0.004 0.049 2217 Dihedral : 5.256 39.304 1863 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.57 % Allowed : 16.94 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1554 helix: 1.47 (0.48), residues: 126 sheet: 0.02 (0.21), residues: 588 loop : -0.64 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 97 TYR 0.017 0.001 TYR H 97 PHE 0.017 0.002 PHE F 592 TRP 0.012 0.001 TRP Y 36 HIS 0.003 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00406 (12573) covalent geometry : angle 0.59072 (17112) SS BOND : bond 0.00288 ( 21) SS BOND : angle 1.26741 ( 42) hydrogen bonds : bond 0.04387 ( 397) hydrogen bonds : angle 4.50652 ( 1149) link_BETA1-4 : bond 0.00303 ( 3) link_BETA1-4 : angle 2.28910 ( 9) link_NAG-ASN : bond 0.00037 ( 3) link_NAG-ASN : angle 1.09027 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8213 (m-30) cc_final: 0.7966 (m-30) REVERT: H 19 ARG cc_start: 0.7116 (ttm170) cc_final: 0.6137 (ttm170) REVERT: H 61 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6609 (m-30) REVERT: H 85 MET cc_start: 0.7148 (ptp) cc_final: 0.6717 (ptp) REVERT: A 228 ASN cc_start: 0.8557 (t0) cc_final: 0.8264 (t0) REVERT: D 596 ARG cc_start: 0.8505 (mtt90) cc_final: 0.8264 (mtt90) REVERT: U 51 ILE cc_start: 0.8312 (mm) cc_final: 0.8100 (mt) REVERT: U 69 LYS cc_start: 0.8199 (tttm) cc_final: 0.7993 (tttp) REVERT: C 188 GLN cc_start: 0.6072 (tp40) cc_final: 0.5668 (mm-40) REVERT: C 228 ASN cc_start: 0.8547 (t0) cc_final: 0.8225 (t0) REVERT: E 120 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7691 (mt-10) REVERT: E 188 GLN cc_start: 0.6083 (tp40) cc_final: 0.5672 (mm-40) REVERT: E 228 ASN cc_start: 0.8476 (t0) cc_final: 0.8263 (t0) REVERT: P 61 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6309 (m-30) REVERT: Y 82 TYR cc_start: 0.7872 (m-80) cc_final: 0.7568 (m-80) outliers start: 46 outliers final: 35 residues processed: 225 average time/residue: 0.1157 time to fit residues: 37.6772 Evaluate side-chains 240 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 61 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.187735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149074 restraints weight = 15133.787| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.78 r_work: 0.3394 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12600 Z= 0.173 Angle : 0.619 7.521 17172 Z= 0.319 Chirality : 0.044 0.146 1872 Planarity : 0.004 0.049 2217 Dihedral : 4.961 27.018 1857 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.03 % Allowed : 17.17 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1554 helix: 1.46 (0.48), residues: 126 sheet: -0.02 (0.21), residues: 588 loop : -0.69 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 97 TYR 0.019 0.001 TYR P 82 PHE 0.017 0.002 PHE F 592 TRP 0.013 0.001 TRP Y 36 HIS 0.003 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00425 (12573) covalent geometry : angle 0.61323 (17112) SS BOND : bond 0.00392 ( 21) SS BOND : angle 1.34951 ( 42) hydrogen bonds : bond 0.04483 ( 397) hydrogen bonds : angle 4.50557 ( 1149) link_BETA1-4 : bond 0.00250 ( 3) link_BETA1-4 : angle 2.32392 ( 9) link_NAG-ASN : bond 0.00041 ( 3) link_NAG-ASN : angle 1.10424 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 34 TYR cc_start: 0.8569 (m-80) cc_final: 0.8308 (m-80) REVERT: H 61 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6590 (m-30) REVERT: H 85 MET cc_start: 0.7178 (ptp) cc_final: 0.6740 (ptp) REVERT: A 228 ASN cc_start: 0.8524 (t0) cc_final: 0.8191 (t0) REVERT: D 596 ARG cc_start: 0.8512 (mtt90) cc_final: 0.8263 (mtt90) REVERT: F 591 ASP cc_start: 0.8487 (m-30) cc_final: 0.8208 (m-30) REVERT: U 51 ILE cc_start: 0.8265 (mm) cc_final: 0.8041 (mt) REVERT: U 109 LYS cc_start: 0.7186 (tppt) cc_final: 0.6842 (tppt) REVERT: C 188 GLN cc_start: 0.6090 (tp40) cc_final: 0.5716 (mm-40) REVERT: C 228 ASN cc_start: 0.8589 (t0) cc_final: 0.8276 (t0) REVERT: E 120 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7741 (mt-10) REVERT: E 188 GLN cc_start: 0.6035 (tp40) cc_final: 0.5675 (mm-40) REVERT: E 228 ASN cc_start: 0.8521 (t0) cc_final: 0.8304 (t0) REVERT: P 34 MET cc_start: 0.8896 (mmp) cc_final: 0.8476 (mmp) outliers start: 39 outliers final: 35 residues processed: 230 average time/residue: 0.1181 time to fit residues: 39.1859 Evaluate side-chains 237 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 77 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 72 optimal weight: 0.0770 chunk 125 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.192501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.156457 restraints weight = 14825.670| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.19 r_work: 0.3513 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12600 Z= 0.109 Angle : 0.587 7.734 17172 Z= 0.303 Chirality : 0.043 0.156 1872 Planarity : 0.004 0.050 2217 Dihedral : 4.702 25.707 1857 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.18 % Allowed : 17.64 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.21), residues: 1554 helix: 1.81 (0.48), residues: 126 sheet: 0.08 (0.22), residues: 585 loop : -0.64 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 19 TYR 0.018 0.001 TYR H 62 PHE 0.014 0.001 PHE Y 29 TRP 0.011 0.001 TRP Y 36 HIS 0.001 0.000 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00248 (12573) covalent geometry : angle 0.58182 (17112) SS BOND : bond 0.00235 ( 21) SS BOND : angle 1.18826 ( 42) hydrogen bonds : bond 0.03829 ( 397) hydrogen bonds : angle 4.44995 ( 1149) link_BETA1-4 : bond 0.00338 ( 3) link_BETA1-4 : angle 2.32382 ( 9) link_NAG-ASN : bond 0.00191 ( 3) link_NAG-ASN : angle 1.19048 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.7810 (tp) cc_final: 0.7550 (mt) REVERT: H 19 ARG cc_start: 0.7194 (ttm170) cc_final: 0.6982 (ttt90) REVERT: H 61 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6399 (m-30) REVERT: H 85 MET cc_start: 0.7075 (ptp) cc_final: 0.6624 (ptp) REVERT: A 228 ASN cc_start: 0.8411 (t0) cc_final: 0.8118 (t0) REVERT: B 596 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8101 (mtt90) REVERT: D 596 ARG cc_start: 0.8425 (mtt90) cc_final: 0.7911 (mtt90) REVERT: U 109 LYS cc_start: 0.7066 (tppt) cc_final: 0.6782 (tppt) REVERT: C 188 GLN cc_start: 0.5969 (tp40) cc_final: 0.5650 (mm-40) REVERT: C 228 ASN cc_start: 0.8515 (t0) cc_final: 0.8205 (t0) REVERT: E 188 GLN cc_start: 0.6002 (tp40) cc_final: 0.5688 (mm-40) REVERT: E 228 ASN cc_start: 0.8537 (t0) cc_final: 0.8312 (t0) REVERT: P 34 MET cc_start: 0.8817 (mmp) cc_final: 0.8371 (mmp) REVERT: P 61 ASP cc_start: 0.6382 (OUTLIER) cc_final: 0.6071 (m-30) REVERT: P 93 THR cc_start: 0.8709 (p) cc_final: 0.8484 (p) REVERT: Y 18 LEU cc_start: 0.8227 (tp) cc_final: 0.7594 (mp) outliers start: 28 outliers final: 25 residues processed: 211 average time/residue: 0.1182 time to fit residues: 35.9976 Evaluate side-chains 220 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain H residue 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 545 GLU Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 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 106 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 0.0670 chunk 102 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 516 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.191287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.152591 restraints weight = 15076.087| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.74 r_work: 0.3447 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12600 Z= 0.113 Angle : 0.580 7.980 17172 Z= 0.302 Chirality : 0.043 0.141 1872 Planarity : 0.004 0.049 2217 Dihedral : 4.616 25.399 1857 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.33 % Allowed : 18.18 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.21), residues: 1554 helix: 1.90 (0.48), residues: 126 sheet: 0.11 (0.22), residues: 576 loop : -0.61 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 97 TYR 0.014 0.001 TYR P 82 PHE 0.015 0.001 PHE Y 29 TRP 0.012 0.001 TRP H 36 HIS 0.001 0.000 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00264 (12573) covalent geometry : angle 0.57561 (17112) SS BOND : bond 0.00239 ( 21) SS BOND : angle 1.14070 ( 42) hydrogen bonds : bond 0.03785 ( 397) hydrogen bonds : angle 4.37843 ( 1149) link_BETA1-4 : bond 0.00335 ( 3) link_BETA1-4 : angle 2.28835 ( 9) link_NAG-ASN : bond 0.00166 ( 3) link_NAG-ASN : angle 1.27193 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2717.08 seconds wall clock time: 47 minutes 25.46 seconds (2845.46 seconds total)