Starting phenix.real_space_refine on Sat Sep 12 22:36:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pci_20301/09_2026/6pci_20301.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pci_20301/09_2026/6pci_20301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6pci_20301/09_2026/6pci_20301.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pci_20301/09_2026/6pci_20301.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pci_20301/09_2026/6pci_20301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pci_20301/09_2026/6pci_20301.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pci_20301/09_2026/6pci_20301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pci_20301/09_2026/6pci_20301.map" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 66 5.16 5 C 11925 2.51 5 N 3153 2.21 5 O 3684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18828 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain breaks: 1 Chain: "H" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1033 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "D" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "Q" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "N" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: B, C, E, F, T, U, I, J, L, M, O, P, R, S Time building chain proxies: 3.69, per 1000 atoms: 0.20 Number of scatterers: 18828 At special positions: 0 Unit cell: (156.56, 148.32, 122.57, 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 66 16.00 O 3684 8.00 N 3153 7.00 C 11925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 89 " distance=2.04 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 89 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 95 " distance=2.04 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 257 " " NAG A 402 " - " ASN A 238 " " NAG A 403 " - " ASN A 228 " " NAG A 404 " - " ASN A 268 " " NAG B 401 " - " ASN B 257 " " NAG B 402 " - " ASN B 238 " " NAG B 403 " - " ASN B 228 " " NAG B 404 " - " ASN B 268 " " NAG C 401 " - " ASN C 257 " " NAG C 402 " - " ASN C 238 " " NAG C 403 " - " ASN C 228 " " NAG C 404 " - " ASN C 268 " " NAG G 1 " - " ASN D 563 " " NAG T 1 " - " ASN E 563 " " NAG U 1 " - " ASN F 563 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 702.2 milliseconds 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4314 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 51 sheets defined 13.1% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'H' and resid 62 through 65 removed outlier: 4.082A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.996A pdb=" N SER K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 553 through 576 removed outlier: 4.665A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 Processing helix chain 'Q' and resid 80 through 84 Processing helix chain 'N' and resid 61 through 64 removed outlier: 3.594A pdb=" N LYS N 64 " --> pdb=" O PRO N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing helix chain 'N' and resid 86 through 90 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'I' and resid 62 through 65 removed outlier: 4.081A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.996A pdb=" N SER L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 Processing helix chain 'E' and resid 538 through 541 Processing helix chain 'E' and resid 553 through 576 removed outlier: 4.664A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA E 575 " --> pdb=" O LEU E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 Processing helix chain 'R' and resid 80 through 84 Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.595A pdb=" N LYS O 64 " --> pdb=" O PRO O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 86 through 90 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'J' and resid 62 through 65 removed outlier: 4.082A pdb=" N LYS J 65 " --> pdb=" O ASP J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.997A pdb=" N SER M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 536 Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 553 through 576 removed outlier: 4.665A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 Processing helix chain 'S' and resid 80 through 84 Processing helix chain 'P' and resid 61 through 64 removed outlier: 3.595A pdb=" N LYS P 64 " --> pdb=" O PRO P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 64' Processing helix chain 'P' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA2, first strand: chain 'D' and resid 543 through 548 removed outlier: 4.029A pdb=" N MET D 548 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 515 " --> pdb=" O MET D 548 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 165 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 114 removed outlier: 7.124A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.216A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 272 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 274 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.524A pdb=" N GLU H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.524A pdb=" N GLU H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS H 96 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP H 121 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS H 98 " --> pdb=" O ASP H 119 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 117 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'K' and resid 12 through 14 removed outlier: 6.844A pdb=" N ALA K 13 " --> pdb=" O LYS K 107 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA K 34 " --> pdb=" O GLN K 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'Q' and resid 10 through 13 removed outlier: 3.617A pdb=" N ALA Q 85 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL Q 86 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE Q 34 " --> pdb=" O SER Q 50 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER Q 50 " --> pdb=" O PHE Q 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 10 through 13 removed outlier: 3.617A pdb=" N ALA Q 85 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.617A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AC1, first strand: chain 'E' and resid 543 through 548 removed outlier: 4.029A pdb=" N MET E 548 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU E 515 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 165 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AC3, first strand: chain 'B' and resid 107 through 114 removed outlier: 7.124A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 240 through 242 removed outlier: 7.216A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 272 " --> pdb=" O TYR I 115 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR I 115 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 274 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER I 113 " --> pdb=" O ILE B 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.524A pdb=" N GLU I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.524A pdb=" N GLU I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY I 10 " --> pdb=" O THR I 128 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET I 34 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY I 10 " --> pdb=" O THR I 128 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS I 96 " --> pdb=" O TRP I 121 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP I 121 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS I 98 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA I 117 " --> pdb=" O LEU I 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.844A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.617A pdb=" N ALA R 85 " --> pdb=" O LEU R 105 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL R 86 " --> pdb=" O GLN R 39 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE R 34 " --> pdb=" O SER R 50 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER R 50 " --> pdb=" O PHE R 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP R 36 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.617A pdb=" N ALA R 85 " --> pdb=" O LEU R 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.616A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 38 Processing sheet with id=AD9, first strand: chain 'F' and resid 543 through 548 removed outlier: 4.029A pdb=" N MET F 548 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU F 515 " --> pdb=" O MET F 548 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 165 " --> pdb=" O TYR C 162 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AE2, first strand: chain 'C' and resid 107 through 114 removed outlier: 7.125A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 240 through 242 removed outlier: 7.217A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS C 272 " --> pdb=" O TYR J 115 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 274 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.525A pdb=" N GLU J 5 " --> pdb=" O ALA J 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 81 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.525A pdb=" N GLU J 5 " --> pdb=" O ALA J 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 81 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY J 10 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET J 34 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY J 10 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS J 96 " --> pdb=" O TRP J 121 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP J 121 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS J 98 " --> pdb=" O ASP J 119 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA J 117 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'M' and resid 12 through 14 removed outlier: 6.843A pdb=" N ALA M 13 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA M 34 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.616A pdb=" N ALA S 85 " --> pdb=" O LEU S 105 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL S 86 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE S 34 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER S 50 " --> pdb=" O PHE S 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.616A pdb=" N ALA S 85 " --> pdb=" O LEU S 105 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.616A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) 706 hydrogen bonds defined for protein. 1749 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: 3.78 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3167 1.32 - 1.45: 5691 1.45 - 1.57: 10321 1.57 - 1.70: 0 1.70 - 1.83: 87 Bond restraints: 19266 Sorted by residual: bond pdb=" C ALA E 507 " pdb=" N GLN E 508 " ideal model delta sigma weight residual 1.329 1.234 0.095 3.03e-02 1.09e+03 9.81e+00 bond pdb=" C ALA F 507 " pdb=" N GLN F 508 " ideal model delta sigma weight residual 1.329 1.234 0.095 3.03e-02 1.09e+03 9.78e+00 bond pdb=" C ALA D 507 " pdb=" N GLN D 508 " ideal model delta sigma weight residual 1.329 1.234 0.094 3.03e-02 1.09e+03 9.71e+00 bond pdb=" N PHE F 517 " pdb=" CA PHE F 517 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.29e-02 6.01e+03 6.39e+00 bond pdb=" N PHE D 517 " pdb=" CA PHE D 517 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.29e-02 6.01e+03 6.20e+00 ... (remaining 19261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 24646 2.06 - 4.13: 1333 4.13 - 6.19: 139 6.19 - 8.25: 45 8.25 - 10.32: 9 Bond angle restraints: 26172 Sorted by residual: angle pdb=" C GLY Q 51 " pdb=" N THR Q 52 " pdb=" CA THR Q 52 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C GLY R 51 " pdb=" N THR R 52 " pdb=" CA THR R 52 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C GLY S 51 " pdb=" N THR S 52 " pdb=" CA THR S 52 " ideal model delta sigma weight residual 121.54 129.17 -7.63 1.91e+00 2.74e-01 1.60e+01 angle pdb=" N ASN B 257 " pdb=" CA ASN B 257 " pdb=" CB ASN B 257 " ideal model delta sigma weight residual 110.28 116.38 -6.10 1.55e+00 4.16e-01 1.55e+01 angle pdb=" N ASN C 257 " pdb=" CA ASN C 257 " pdb=" CB ASN C 257 " ideal model delta sigma weight residual 110.28 116.36 -6.08 1.55e+00 4.16e-01 1.54e+01 ... (remaining 26167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.83: 9675 9.83 - 19.66: 1136 19.66 - 29.49: 169 29.49 - 39.32: 63 39.32 - 49.15: 63 Dihedral angle restraints: 11106 sinusoidal: 4311 harmonic: 6795 Sorted by residual: dihedral pdb=" CA SER M 30 " pdb=" C SER M 30 " pdb=" N ASN M 31 " pdb=" CA ASN M 31 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA SER K 30 " pdb=" C SER K 30 " pdb=" N ASN K 31 " pdb=" CA ASN K 31 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA SER L 30 " pdb=" C SER L 30 " pdb=" N ASN L 31 " pdb=" CA ASN L 31 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 11103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2703 0.103 - 0.206: 231 0.206 - 0.309: 9 0.309 - 0.412: 6 0.412 - 0.515: 3 Chirality restraints: 2952 Sorted by residual: chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 268 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" C1 NAG A 404 " pdb=" ND2 ASN A 268 " pdb=" C2 NAG A 404 " pdb=" O5 NAG A 404 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" C1 NAG B 404 " pdb=" ND2 ASN B 268 " pdb=" C2 NAG B 404 " pdb=" O5 NAG B 404 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.57e+00 ... (remaining 2949 not shown) Planarity restraints: 3330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 257 " -0.006 2.00e-02 2.50e+03 2.35e-02 6.92e+00 pdb=" CG ASN B 257 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B 257 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN B 257 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 92 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.84e+00 pdb=" C LYS K 92 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS K 92 " -0.017 2.00e-02 2.50e+03 pdb=" N SER K 93 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 257 " -0.006 2.00e-02 2.50e+03 2.34e-02 6.84e+00 pdb=" CG ASN C 257 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN C 257 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN C 257 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " -0.020 2.00e-02 2.50e+03 ... (remaining 3327 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4982 2.79 - 3.32: 15956 3.32 - 3.85: 32024 3.85 - 4.37: 36136 4.37 - 4.90: 61036 Nonbonded interactions: 150134 Sorted by model distance: nonbonded pdb=" O GLY A 224 " pdb=" OG1 THR A 230 " model vdw 2.268 3.040 nonbonded pdb=" O GLY B 224 " pdb=" OG1 THR B 230 " model vdw 2.269 3.040 nonbonded pdb=" O GLY C 224 " pdb=" OG1 THR C 230 " model vdw 2.269 3.040 nonbonded pdb=" NE2 GLN L 90 " pdb=" O SER L 93 " model vdw 2.274 3.120 nonbonded pdb=" NE2 GLN M 90 " pdb=" O SER M 93 " model vdw 2.277 3.120 ... (remaining 150129 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 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.590 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.009 0.095 19314 Z= 0.436 Angle : 1.088 12.772 26295 Z= 0.585 Chirality : 0.061 0.515 2952 Planarity : 0.007 0.050 3315 Dihedral : 8.957 46.734 6729 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -2.72 (0.16), residues: 2340 helix: -2.31 (0.30), residues: 201 sheet: -1.81 (0.16), residues: 933 loop : -1.61 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 164 TYR 0.028 0.004 TYR A 109 PHE 0.025 0.004 PHE D 582 TRP 0.039 0.004 TRP A 104 HIS 0.009 0.003 HIS E 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00932 / 0.44 (19266) covalent geometry : angle 1.05240 / 0.58 (26172) SS BOND : bond 0.00793 / 0.50 ( 21) SS BOND : angle 1.88223 / 1.15 ( 42) hydrogen bonds : bond 0.26686 / 18.42 ( 622) hydrogen bonds : angle 10.66242 / 7.38 ( 1749) link_ALPHA1-3 : bond 0.00069 / 0.03 ( 3) link_ALPHA1-3 : angle 1.77423 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00049 / 0.03 ( 3) link_ALPHA1-6 : angle 1.68010 / 0.95 ( 9) link_BETA1-4 : bond 0.00536 / 0.33 ( 6) link_BETA1-4 : angle 4.23777 / 2.73 ( 18) link_NAG-ASN : bond 0.00537 / 0.33 ( 15) link_NAG-ASN : angle 6.01395 / 3.90 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 774 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8994 (mt0) cc_final: 0.8720 (mt0) REVERT: A 106 GLU cc_start: 0.8709 (tp30) cc_final: 0.7930 (tp30) REVERT: A 117 ASP cc_start: 0.8719 (p0) cc_final: 0.8373 (p0) REVERT: A 261 TYR cc_start: 0.7921 (m-10) cc_final: 0.7712 (m-10) REVERT: H 12 VAL cc_start: 0.6935 (t) cc_final: 0.6212 (t) REVERT: H 45 LEU cc_start: 0.7668 (tp) cc_final: 0.7316 (tp) REVERT: H 57 LYS cc_start: 0.8460 (tppt) cc_final: 0.8247 (tttm) REVERT: H 80 TYR cc_start: 0.8590 (m-10) cc_final: 0.8337 (m-80) REVERT: K 36 TYR cc_start: 0.8096 (m-10) cc_final: 0.7896 (m-80) REVERT: K 47 LEU cc_start: 0.9327 (mt) cc_final: 0.8912 (mt) REVERT: K 78 LEU cc_start: 0.7274 (mt) cc_final: 0.6767 (mt) REVERT: K 89 GLN cc_start: 0.8357 (tt0) cc_final: 0.7876 (tt0) REVERT: K 92 LYS cc_start: 0.8837 (tttt) cc_final: 0.8466 (tppt) REVERT: K 104 LEU cc_start: 0.7016 (tp) cc_final: 0.5617 (tp) REVERT: D 532 ILE cc_start: 0.9440 (mt) cc_final: 0.9156 (pt) REVERT: D 597 TRP cc_start: 0.7620 (t-100) cc_final: 0.7270 (t-100) REVERT: Q 20 THR cc_start: 0.8418 (p) cc_final: 0.7608 (p) REVERT: Q 38 GLN cc_start: 0.8944 (tt0) cc_final: 0.8671 (tt0) REVERT: Q 43 GLN cc_start: 0.8579 (mm-40) cc_final: 0.7907 (mm-40) REVERT: Q 54 THR cc_start: 0.9418 (m) cc_final: 0.9091 (p) REVERT: Q 79 LEU cc_start: 0.8426 (mt) cc_final: 0.7668 (mt) REVERT: N 77 GLN cc_start: 0.8460 (mt0) cc_final: 0.8160 (mt0) REVERT: N 100 TRP cc_start: 0.9139 (t-100) cc_final: 0.8791 (t-100) REVERT: B 62 GLN cc_start: 0.8965 (mt0) cc_final: 0.8708 (mt0) REVERT: B 106 GLU cc_start: 0.8682 (tp30) cc_final: 0.8071 (tp30) REVERT: B 117 ASP cc_start: 0.8803 (p0) cc_final: 0.8409 (p0) REVERT: B 178 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8724 (mt-10) REVERT: B 272 LYS cc_start: 0.6177 (pttt) cc_final: 0.5926 (pttm) REVERT: I 34 MET cc_start: 0.7829 (mmm) cc_final: 0.7552 (mmp) REVERT: I 45 LEU cc_start: 0.7841 (tp) cc_final: 0.7497 (tp) REVERT: I 57 LYS cc_start: 0.8524 (tppt) cc_final: 0.8304 (tttm) REVERT: I 64 VAL cc_start: 0.9131 (m) cc_final: 0.8481 (t) REVERT: I 80 TYR cc_start: 0.8694 (m-10) cc_final: 0.8438 (m-80) REVERT: I 94 TYR cc_start: 0.7276 (m-10) cc_final: 0.6767 (m-10) REVERT: I 112 HIS cc_start: 0.6150 (t-90) cc_final: 0.5643 (t-90) REVERT: L 36 TYR cc_start: 0.8174 (m-10) cc_final: 0.7947 (m-80) REVERT: L 73 LEU cc_start: 0.8171 (tp) cc_final: 0.7892 (tp) REVERT: L 89 GLN cc_start: 0.8356 (tt0) cc_final: 0.8124 (tt0) REVERT: L 92 LYS cc_start: 0.8862 (tttt) cc_final: 0.8328 (tppt) REVERT: E 532 ILE cc_start: 0.9454 (mt) cc_final: 0.9113 (pt) REVERT: E 555 ILE cc_start: 0.9015 (mt) cc_final: 0.8761 (mp) REVERT: E 597 TRP cc_start: 0.7708 (t-100) cc_final: 0.7349 (t-100) REVERT: R 13 LEU cc_start: 0.8494 (mp) cc_final: 0.8281 (mp) REVERT: R 34 PHE cc_start: 0.8451 (m-10) cc_final: 0.7830 (m-10) REVERT: R 61 ASP cc_start: 0.8456 (p0) cc_final: 0.8083 (t0) REVERT: O 35 ASN cc_start: 0.8769 (m-40) cc_final: 0.8430 (m-40) REVERT: O 58 ASN cc_start: 0.8735 (t0) cc_final: 0.8520 (t0) REVERT: O 100 TRP cc_start: 0.9170 (t-100) cc_final: 0.8495 (t-100) REVERT: C 62 GLN cc_start: 0.8834 (mt0) cc_final: 0.8569 (mt0) REVERT: C 78 ASP cc_start: 0.8126 (t0) cc_final: 0.7896 (t0) REVERT: C 106 GLU cc_start: 0.8653 (tp30) cc_final: 0.7899 (tp30) REVERT: C 117 ASP cc_start: 0.8790 (p0) cc_final: 0.8394 (p0) REVERT: C 163 ASP cc_start: 0.9355 (t0) cc_final: 0.9094 (t0) REVERT: J 12 VAL cc_start: 0.6377 (t) cc_final: 0.6072 (t) REVERT: J 36 TRP cc_start: 0.6997 (m100) cc_final: 0.5896 (m100) REVERT: J 46 GLU cc_start: 0.8744 (pt0) cc_final: 0.8226 (pm20) REVERT: J 57 LYS cc_start: 0.8653 (tppt) cc_final: 0.8234 (tttm) REVERT: J 64 VAL cc_start: 0.9157 (m) cc_final: 0.8604 (t) REVERT: J 80 TYR cc_start: 0.8698 (m-10) cc_final: 0.8343 (m-80) REVERT: J 83 MET cc_start: 0.8601 (mtt) cc_final: 0.8362 (mmm) REVERT: J 102 GLN cc_start: 0.8060 (mt0) cc_final: 0.7553 (mt0) REVERT: M 31 ASN cc_start: 0.7167 (p0) cc_final: 0.6780 (m-40) REVERT: M 37 GLN cc_start: 0.7924 (tt0) cc_final: 0.7699 (tt0) REVERT: M 58 VAL cc_start: 0.7348 (t) cc_final: 0.7058 (p) REVERT: M 73 LEU cc_start: 0.8001 (tp) cc_final: 0.7634 (tp) REVERT: M 85 THR cc_start: 0.6518 (m) cc_final: 0.6316 (p) REVERT: M 86 TYR cc_start: 0.6756 (m-10) cc_final: 0.6212 (m-80) REVERT: M 92 LYS cc_start: 0.8977 (tttt) cc_final: 0.8522 (ttmm) REVERT: F 581 THR cc_start: 0.9622 (m) cc_final: 0.9023 (p) REVERT: S 20 THR cc_start: 0.8466 (p) cc_final: 0.7757 (p) REVERT: S 21 LEU cc_start: 0.8402 (tp) cc_final: 0.8163 (tp) REVERT: S 34 PHE cc_start: 0.7778 (m-10) cc_final: 0.7393 (m-10) REVERT: S 47 LEU cc_start: 0.9022 (tp) cc_final: 0.8803 (tt) REVERT: S 61 ASP cc_start: 0.8279 (p0) cc_final: 0.7803 (t0) REVERT: S 84 PHE cc_start: 0.7585 (t80) cc_final: 0.7117 (t80) REVERT: S 97 TYR cc_start: 0.8641 (m-80) cc_final: 0.8429 (m-80) REVERT: P 60 ASN cc_start: 0.9117 (t0) cc_final: 0.8648 (t0) REVERT: P 100 TRP cc_start: 0.9135 (t-100) cc_final: 0.8695 (t-100) REVERT: P 112 ASP cc_start: 0.8945 (p0) cc_final: 0.8272 (p0) outliers start: 0 outliers final: 0 residues processed: 774 average time/residue: 0.1617 time to fit residues: 180.2155 Evaluate side-chains 472 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN A 255 GLN H 3 GLN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 255 GLN I 102 GLN ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN C 188 GLN C 255 GLN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN S 43 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.108271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.077951 restraints weight = 54058.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.080454 restraints weight = 29347.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.082048 restraints weight = 20282.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.083002 restraints weight = 16278.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.083495 restraints weight = 14287.216| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19314 Z= 0.148 Angle : 0.720 9.648 26295 Z= 0.369 Chirality : 0.049 0.374 2952 Planarity : 0.005 0.052 3315 Dihedral : 6.134 26.305 2592 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.78 (0.16), residues: 2340 helix: -0.88 (0.33), residues: 201 sheet: -1.15 (0.16), residues: 855 loop : -1.19 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 62 TYR 0.031 0.002 TYR M 96 PHE 0.037 0.002 PHE H 68 TRP 0.017 0.001 TRP A 104 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (19266) covalent geometry : angle 0.69241 / 0.36 (26172) SS BOND : bond 0.00501 / 0.30 ( 21) SS BOND : angle 1.07258 / 0.68 ( 42) hydrogen bonds : bond 0.04542 / 3.13 ( 622) hydrogen bonds : angle 7.39155 / 5.14 ( 1749) link_ALPHA1-3 : bond 0.00546 / 0.27 ( 3) link_ALPHA1-3 : angle 1.39553 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00867 / 0.45 ( 3) link_ALPHA1-6 : angle 1.65124 / 0.92 ( 9) link_BETA1-4 : bond 0.00530 / 0.27 ( 6) link_BETA1-4 : angle 3.06712 / 1.94 ( 18) link_NAG-ASN : bond 0.00612 / 0.39 ( 15) link_NAG-ASN : angle 4.28689 / 2.69 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 707 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8241 (t70) cc_final: 0.7943 (t70) REVERT: A 117 ASP cc_start: 0.8538 (p0) cc_final: 0.8201 (p0) REVERT: A 150 ASP cc_start: 0.8692 (m-30) cc_final: 0.8488 (m-30) REVERT: A 272 LYS cc_start: 0.5709 (pttt) cc_final: 0.5392 (ttmm) REVERT: H 12 VAL cc_start: 0.7046 (t) cc_final: 0.6437 (t) REVERT: H 45 LEU cc_start: 0.7618 (tp) cc_final: 0.7326 (tp) REVERT: H 86 LEU cc_start: 0.9138 (mt) cc_final: 0.8931 (mt) REVERT: K 46 LEU cc_start: 0.8987 (pt) cc_final: 0.8764 (pt) REVERT: K 81 GLU cc_start: 0.8707 (mp0) cc_final: 0.8371 (mp0) REVERT: K 82 ASP cc_start: 0.6754 (m-30) cc_final: 0.6177 (t0) REVERT: K 86 TYR cc_start: 0.5978 (m-10) cc_final: 0.3861 (m-10) REVERT: D 532 ILE cc_start: 0.9308 (mt) cc_final: 0.9092 (pt) REVERT: D 560 GLN cc_start: 0.9220 (tp40) cc_final: 0.8419 (tp40) REVERT: D 581 THR cc_start: 0.9606 (m) cc_final: 0.9353 (p) REVERT: D 592 PHE cc_start: 0.8444 (t80) cc_final: 0.8016 (t80) REVERT: Q 21 LEU cc_start: 0.8285 (tp) cc_final: 0.7926 (tp) REVERT: Q 61 ASP cc_start: 0.8002 (p0) cc_final: 0.7725 (p0) REVERT: Q 79 LEU cc_start: 0.8366 (mt) cc_final: 0.7887 (mt) REVERT: N 15 SER cc_start: 0.8789 (m) cc_final: 0.8478 (p) REVERT: N 100 TRP cc_start: 0.9101 (t-100) cc_final: 0.8628 (t-100) REVERT: N 112 ASP cc_start: 0.9018 (p0) cc_final: 0.8551 (p0) REVERT: B 62 GLN cc_start: 0.9283 (mt0) cc_final: 0.8501 (mt0) REVERT: B 103 GLU cc_start: 0.8248 (tt0) cc_final: 0.7864 (tt0) REVERT: B 117 ASP cc_start: 0.8554 (p0) cc_final: 0.8125 (p0) REVERT: I 34 MET cc_start: 0.7676 (mmm) cc_final: 0.7391 (mmp) REVERT: I 46 GLU cc_start: 0.8593 (pt0) cc_final: 0.8259 (pm20) REVERT: I 86 LEU cc_start: 0.9068 (mt) cc_final: 0.8839 (mt) REVERT: L 24 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7581 (mmm-85) REVERT: L 31 ASN cc_start: 0.7037 (p0) cc_final: 0.6410 (m-40) REVERT: L 36 TYR cc_start: 0.8260 (m-10) cc_final: 0.7997 (m-80) REVERT: L 70 ASP cc_start: 0.7400 (t0) cc_final: 0.6811 (p0) REVERT: L 73 LEU cc_start: 0.8324 (tp) cc_final: 0.8026 (tp) REVERT: L 89 GLN cc_start: 0.8286 (tt0) cc_final: 0.7981 (tt0) REVERT: L 90 GLN cc_start: 0.7793 (tp40) cc_final: 0.7044 (tp40) REVERT: E 532 ILE cc_start: 0.9311 (mt) cc_final: 0.9042 (pt) REVERT: E 534 TYR cc_start: 0.9285 (t80) cc_final: 0.9004 (t80) REVERT: E 573 LEU cc_start: 0.9612 (mt) cc_final: 0.9371 (mt) REVERT: E 581 THR cc_start: 0.9664 (m) cc_final: 0.9281 (p) REVERT: R 18 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7743 (ttp80) REVERT: R 21 LEU cc_start: 0.7949 (tt) cc_final: 0.7511 (mm) REVERT: R 36 TRP cc_start: 0.8504 (m100) cc_final: 0.8244 (m100) REVERT: R 61 ASP cc_start: 0.8268 (p0) cc_final: 0.8058 (t0) REVERT: O 58 ASN cc_start: 0.8753 (t0) cc_final: 0.8268 (t0) REVERT: O 100 TRP cc_start: 0.9116 (t-100) cc_final: 0.8625 (t-100) REVERT: C 62 GLN cc_start: 0.9305 (mt0) cc_final: 0.8406 (mt0) REVERT: C 68 LEU cc_start: 0.9432 (mt) cc_final: 0.9214 (mt) REVERT: C 117 ASP cc_start: 0.8499 (p0) cc_final: 0.8241 (p0) REVERT: C 273 LEU cc_start: 0.7654 (mp) cc_final: 0.7327 (mp) REVERT: J 12 VAL cc_start: 0.6893 (t) cc_final: 0.6600 (t) REVERT: J 36 TRP cc_start: 0.6870 (m100) cc_final: 0.5924 (m100) REVERT: J 46 GLU cc_start: 0.8727 (pt0) cc_final: 0.8313 (pm20) REVERT: J 57 LYS cc_start: 0.8837 (tppt) cc_final: 0.8439 (tttm) REVERT: J 83 MET cc_start: 0.8769 (mtt) cc_final: 0.8407 (mmm) REVERT: J 102 GLN cc_start: 0.8153 (mt0) cc_final: 0.7691 (mt0) REVERT: J 128 THR cc_start: 0.9154 (m) cc_final: 0.8829 (t) REVERT: M 24 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.6940 (mmm-85) REVERT: M 31 ASN cc_start: 0.7207 (p0) cc_final: 0.6896 (m-40) REVERT: M 58 VAL cc_start: 0.7241 (t) cc_final: 0.6960 (p) REVERT: M 73 LEU cc_start: 0.8159 (tp) cc_final: 0.7668 (tp) REVERT: M 86 TYR cc_start: 0.6348 (m-10) cc_final: 0.5961 (m-80) REVERT: M 90 GLN cc_start: 0.7710 (tp40) cc_final: 0.7354 (tp40) REVERT: M 104 LEU cc_start: 0.7686 (tp) cc_final: 0.6530 (tp) REVERT: F 581 THR cc_start: 0.9652 (m) cc_final: 0.9364 (p) REVERT: S 4 LEU cc_start: 0.8671 (mt) cc_final: 0.8299 (mt) REVERT: S 61 ASP cc_start: 0.8137 (p0) cc_final: 0.7811 (t0) REVERT: S 62 ARG cc_start: 0.8437 (ptt-90) cc_final: 0.7655 (ptp90) REVERT: S 78 ARG cc_start: 0.8385 (ttp-170) cc_final: 0.7854 (ttp-170) REVERT: S 96 LEU cc_start: 0.9382 (mt) cc_final: 0.9177 (mp) REVERT: S 97 TYR cc_start: 0.8619 (m-80) cc_final: 0.8377 (m-80) REVERT: P 15 SER cc_start: 0.8908 (m) cc_final: 0.8405 (p) REVERT: P 32 TYR cc_start: 0.8794 (m-10) cc_final: 0.8234 (m-10) REVERT: P 60 ASN cc_start: 0.9204 (t0) cc_final: 0.8722 (t0) REVERT: P 100 TRP cc_start: 0.9075 (t-100) cc_final: 0.8629 (t-100) REVERT: P 111 MET cc_start: 0.8504 (mtm) cc_final: 0.8057 (mtt) REVERT: P 112 ASP cc_start: 0.8954 (p0) cc_final: 0.8506 (p0) outliers start: 0 outliers final: 0 residues processed: 707 average time/residue: 0.1350 time to fit residues: 145.1528 Evaluate side-chains 503 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 148 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN I 3 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN M 90 GLN ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.105014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.074648 restraints weight = 54516.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076962 restraints weight = 29778.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078434 restraints weight = 20801.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.079288 restraints weight = 16818.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.079831 restraints weight = 14907.773| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 19314 Z= 0.265 Angle : 0.766 11.601 26295 Z= 0.386 Chirality : 0.049 0.378 2952 Planarity : 0.005 0.043 3315 Dihedral : 6.002 24.087 2592 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.54 (0.17), residues: 2340 helix: 0.01 (0.36), residues: 183 sheet: -1.06 (0.16), residues: 912 loop : -1.06 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 38 TYR 0.028 0.003 TYR H 114 PHE 0.033 0.002 PHE Q 72 TRP 0.015 0.002 TRP O 114 HIS 0.006 0.001 HIS I 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.27 (19266) covalent geometry : angle 0.73763 / 0.38 (26172) SS BOND : bond 0.00624 / 0.36 ( 21) SS BOND : angle 1.49749 / 0.90 ( 42) hydrogen bonds : bond 0.04267 / 2.92 ( 622) hydrogen bonds : angle 6.75416 / 4.69 ( 1749) link_ALPHA1-3 : bond 0.00448 / 0.23 ( 3) link_ALPHA1-3 : angle 1.25886 / 0.71 ( 9) link_ALPHA1-6 : bond 0.00060 / 0.03 ( 3) link_ALPHA1-6 : angle 1.68623 / 0.93 ( 9) link_BETA1-4 : bond 0.00397 / 0.21 ( 6) link_BETA1-4 : angle 2.86898 / 1.84 ( 18) link_NAG-ASN : bond 0.00515 / 0.31 ( 15) link_NAG-ASN : angle 4.50620 / 2.71 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8211 (t70) cc_final: 0.7999 (t-170) REVERT: A 62 GLN cc_start: 0.9169 (mt0) cc_final: 0.8931 (mt0) REVERT: A 78 ASP cc_start: 0.8359 (t70) cc_final: 0.8084 (t70) REVERT: A 117 ASP cc_start: 0.8424 (p0) cc_final: 0.8169 (p0) REVERT: H 102 GLN cc_start: 0.8320 (mt0) cc_final: 0.7569 (mt0) REVERT: H 114 TYR cc_start: 0.6477 (m-10) cc_final: 0.6013 (m-10) REVERT: K 46 LEU cc_start: 0.9119 (pt) cc_final: 0.8829 (pt) REVERT: K 81 GLU cc_start: 0.8630 (mp0) cc_final: 0.8268 (mp0) REVERT: K 89 GLN cc_start: 0.8405 (tt0) cc_final: 0.8081 (tt0) REVERT: D 512 ASN cc_start: 0.9294 (t0) cc_final: 0.9053 (t0) REVERT: D 581 THR cc_start: 0.9640 (m) cc_final: 0.9305 (p) REVERT: D 592 PHE cc_start: 0.8466 (t80) cc_final: 0.8079 (t80) REVERT: Q 43 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7810 (mm-40) REVERT: Q 61 ASP cc_start: 0.8171 (p0) cc_final: 0.7922 (p0) REVERT: N 15 SER cc_start: 0.8789 (m) cc_final: 0.7936 (p) REVERT: N 112 ASP cc_start: 0.8989 (p0) cc_final: 0.8685 (p0) REVERT: B 62 GLN cc_start: 0.9317 (mt0) cc_final: 0.8543 (mt0) REVERT: B 117 ASP cc_start: 0.8527 (p0) cc_final: 0.8228 (p0) REVERT: I 46 GLU cc_start: 0.8701 (pt0) cc_final: 0.8322 (pm20) REVERT: I 59 PHE cc_start: 0.7260 (t80) cc_final: 0.6847 (t80) REVERT: I 76 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8440 (ptpp) REVERT: I 80 TYR cc_start: 0.8315 (m-80) cc_final: 0.7931 (m-80) REVERT: I 86 LEU cc_start: 0.9240 (mt) cc_final: 0.8844 (mt) REVERT: L 31 ASN cc_start: 0.7244 (p0) cc_final: 0.6624 (m-40) REVERT: L 73 LEU cc_start: 0.8428 (tp) cc_final: 0.8074 (tp) REVERT: E 532 ILE cc_start: 0.9375 (mt) cc_final: 0.9125 (pt) REVERT: E 555 ILE cc_start: 0.9154 (mt) cc_final: 0.8864 (mt) REVERT: E 565 THR cc_start: 0.9237 (p) cc_final: 0.8830 (t) REVERT: E 581 THR cc_start: 0.9647 (m) cc_final: 0.9294 (p) REVERT: E 592 PHE cc_start: 0.8502 (t80) cc_final: 0.8127 (t80) REVERT: E 597 TRP cc_start: 0.7471 (t-100) cc_final: 0.7031 (t-100) REVERT: R 18 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7802 (ttp80) REVERT: R 61 ASP cc_start: 0.8312 (p0) cc_final: 0.8010 (t0) REVERT: O 112 ASP cc_start: 0.8817 (p0) cc_final: 0.8610 (p0) REVERT: C 62 GLN cc_start: 0.9101 (mt0) cc_final: 0.8368 (mt0) REVERT: C 68 LEU cc_start: 0.9494 (mt) cc_final: 0.9198 (mt) REVERT: C 117 ASP cc_start: 0.8373 (p0) cc_final: 0.8133 (p0) REVERT: C 172 ARG cc_start: 0.8734 (ttm110) cc_final: 0.8515 (ttm110) REVERT: C 273 LEU cc_start: 0.7657 (mp) cc_final: 0.7391 (mp) REVERT: J 12 VAL cc_start: 0.6863 (t) cc_final: 0.6554 (t) REVERT: J 46 GLU cc_start: 0.8675 (pt0) cc_final: 0.8268 (pm20) REVERT: J 80 TYR cc_start: 0.8198 (m-80) cc_final: 0.7960 (m-80) REVERT: J 83 MET cc_start: 0.8690 (mtt) cc_final: 0.8284 (mmm) REVERT: J 101 LEU cc_start: 0.9051 (tp) cc_final: 0.8836 (tp) REVERT: J 102 GLN cc_start: 0.8177 (mt0) cc_final: 0.7959 (mt0) REVERT: J 128 THR cc_start: 0.9337 (m) cc_final: 0.9050 (t) REVERT: M 24 ARG cc_start: 0.7328 (mmm-85) cc_final: 0.6980 (mmm-85) REVERT: M 31 ASN cc_start: 0.7280 (p0) cc_final: 0.7054 (m-40) REVERT: M 58 VAL cc_start: 0.7600 (t) cc_final: 0.7232 (p) REVERT: M 73 LEU cc_start: 0.8090 (tp) cc_final: 0.7707 (tp) REVERT: M 90 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7560 (tp40) REVERT: F 581 THR cc_start: 0.9651 (m) cc_final: 0.9309 (p) REVERT: F 592 PHE cc_start: 0.8303 (t80) cc_final: 0.7992 (t80) REVERT: S 4 LEU cc_start: 0.8502 (mt) cc_final: 0.8248 (mt) REVERT: S 61 ASP cc_start: 0.8204 (p0) cc_final: 0.7773 (t0) REVERT: P 15 SER cc_start: 0.8889 (m) cc_final: 0.8287 (p) REVERT: P 32 TYR cc_start: 0.8821 (m-10) cc_final: 0.8510 (m-10) REVERT: P 52 HIS cc_start: 0.7978 (t-90) cc_final: 0.7442 (t-90) REVERT: P 60 ASN cc_start: 0.9271 (t0) cc_final: 0.8859 (t0) REVERT: P 111 MET cc_start: 0.8642 (mtm) cc_final: 0.8190 (mtt) REVERT: P 112 ASP cc_start: 0.8865 (p0) cc_final: 0.8553 (p0) outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 0.1343 time to fit residues: 122.6010 Evaluate side-chains 464 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 63 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS H 74 ASN ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN I 82 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 GLN E 567 GLN ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.107080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077686 restraints weight = 54063.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.080524 restraints weight = 29647.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081149 restraints weight = 19132.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.081624 restraints weight = 16410.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.081647 restraints weight = 15505.611| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19314 Z= 0.145 Angle : 0.680 10.053 26295 Z= 0.342 Chirality : 0.047 0.332 2952 Planarity : 0.004 0.041 3315 Dihedral : 5.553 22.434 2592 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.20 % Allowed : 2.56 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.19 (0.17), residues: 2340 helix: 0.40 (0.37), residues: 183 sheet: -0.67 (0.17), residues: 891 loop : -1.00 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 52 TYR 0.032 0.002 TYR I 114 PHE 0.016 0.002 PHE F 582 TRP 0.013 0.001 TRP N 114 HIS 0.009 0.001 HIS I 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (19266) covalent geometry : angle 0.65506 / 0.34 (26172) SS BOND : bond 0.00559 / 0.33 ( 21) SS BOND : angle 1.02684 / 0.65 ( 42) hydrogen bonds : bond 0.03598 / 2.50 ( 622) hydrogen bonds : angle 6.17212 / 4.28 ( 1749) link_ALPHA1-3 : bond 0.00427 / 0.22 ( 3) link_ALPHA1-3 : angle 1.28279 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00469 / 0.23 ( 3) link_ALPHA1-6 : angle 1.51785 / 0.85 ( 9) link_BETA1-4 : bond 0.00415 / 0.21 ( 6) link_BETA1-4 : angle 2.68514 / 1.71 ( 18) link_NAG-ASN : bond 0.00527 / 0.35 ( 15) link_NAG-ASN : angle 4.01911 / 2.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 602 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9175 (mt0) cc_final: 0.8443 (mt0) REVERT: A 117 ASP cc_start: 0.8384 (p0) cc_final: 0.8060 (p0) REVERT: H 114 TYR cc_start: 0.6275 (m-10) cc_final: 0.5646 (m-10) REVERT: K 81 GLU cc_start: 0.8614 (mp0) cc_final: 0.8284 (mp0) REVERT: D 512 ASN cc_start: 0.9174 (t0) cc_final: 0.8968 (t0) REVERT: D 560 GLN cc_start: 0.9251 (tp40) cc_final: 0.8134 (tp40) REVERT: D 581 THR cc_start: 0.9580 (m) cc_final: 0.9267 (p) REVERT: Q 43 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7869 (mm-40) REVERT: Q 61 ASP cc_start: 0.8084 (p0) cc_final: 0.7855 (p0) REVERT: N 15 SER cc_start: 0.8804 (m) cc_final: 0.8530 (p) REVERT: N 52 HIS cc_start: 0.7740 (t-90) cc_final: 0.7022 (t-90) REVERT: B 47 ASP cc_start: 0.6403 (t0) cc_final: 0.5998 (t0) REVERT: B 62 GLN cc_start: 0.9158 (mt0) cc_final: 0.8432 (mt0) REVERT: B 117 ASP cc_start: 0.8490 (p0) cc_final: 0.8078 (p0) REVERT: B 240 THR cc_start: 0.9512 (m) cc_final: 0.9288 (p) REVERT: I 46 GLU cc_start: 0.8635 (pt0) cc_final: 0.8229 (pm20) REVERT: I 59 PHE cc_start: 0.7107 (t80) cc_final: 0.6784 (t80) REVERT: I 76 LYS cc_start: 0.8671 (mtmm) cc_final: 0.8387 (ptpp) REVERT: I 80 TYR cc_start: 0.8193 (m-80) cc_final: 0.7855 (m-10) REVERT: L 31 ASN cc_start: 0.7122 (p0) cc_final: 0.6644 (m-40) REVERT: L 70 ASP cc_start: 0.7195 (t0) cc_final: 0.6592 (p0) REVERT: L 73 LEU cc_start: 0.8375 (tp) cc_final: 0.8012 (tp) REVERT: L 104 LEU cc_start: 0.7730 (tp) cc_final: 0.7318 (tt) REVERT: E 532 ILE cc_start: 0.9208 (mt) cc_final: 0.8888 (pt) REVERT: E 555 ILE cc_start: 0.9073 (mt) cc_final: 0.8810 (mt) REVERT: E 565 THR cc_start: 0.9238 (p) cc_final: 0.8845 (t) REVERT: E 573 LEU cc_start: 0.9609 (mt) cc_final: 0.9398 (mt) REVERT: E 581 THR cc_start: 0.9657 (m) cc_final: 0.9328 (p) REVERT: E 597 TRP cc_start: 0.7448 (t-100) cc_final: 0.7011 (t-100) REVERT: R 18 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7631 (ttp80) REVERT: R 61 ASP cc_start: 0.8298 (p0) cc_final: 0.7939 (t0) REVERT: R 106 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7421 (tm-30) REVERT: O 16 GLU cc_start: 0.8632 (pt0) cc_final: 0.8235 (pt0) REVERT: C 39 HIS cc_start: 0.8374 (t70) cc_final: 0.8066 (t70) REVERT: C 56 LYS cc_start: 0.7513 (mmtm) cc_final: 0.7302 (mmmt) REVERT: C 62 GLN cc_start: 0.8997 (mt0) cc_final: 0.8376 (mt0) REVERT: C 68 LEU cc_start: 0.9407 (mt) cc_final: 0.9030 (mt) REVERT: J 12 VAL cc_start: 0.6809 (t) cc_final: 0.6540 (t) REVERT: J 28 MET cc_start: 0.8475 (tpt) cc_final: 0.8274 (tpt) REVERT: J 36 TRP cc_start: 0.7272 (m100) cc_final: 0.6943 (m100) REVERT: J 43 LYS cc_start: 0.8402 (mppt) cc_final: 0.8184 (mppt) REVERT: J 46 GLU cc_start: 0.8739 (pt0) cc_final: 0.8304 (pm20) REVERT: J 52 ARG cc_start: 0.7654 (mtt90) cc_final: 0.7339 (mtt90) REVERT: J 64 VAL cc_start: 0.9174 (m) cc_final: 0.8598 (t) REVERT: J 82 GLN cc_start: 0.8016 (tp40) cc_final: 0.7761 (tp-100) REVERT: J 83 MET cc_start: 0.8660 (mtt) cc_final: 0.8407 (mmm) REVERT: J 102 GLN cc_start: 0.8221 (mt0) cc_final: 0.7803 (mt0) REVERT: J 128 THR cc_start: 0.9311 (m) cc_final: 0.9075 (t) REVERT: M 55 GLN cc_start: 0.7325 (tm-30) cc_final: 0.7102 (tm-30) REVERT: M 73 LEU cc_start: 0.7975 (tp) cc_final: 0.7503 (tp) REVERT: M 90 GLN cc_start: 0.7804 (tp-100) cc_final: 0.7312 (tp40) REVERT: F 581 THR cc_start: 0.9620 (m) cc_final: 0.9305 (p) REVERT: F 592 PHE cc_start: 0.8261 (t80) cc_final: 0.7887 (t80) REVERT: S 4 LEU cc_start: 0.8456 (mt) cc_final: 0.8194 (mt) REVERT: S 61 ASP cc_start: 0.8183 (p0) cc_final: 0.7688 (t0) REVERT: P 15 SER cc_start: 0.8973 (m) cc_final: 0.8449 (p) REVERT: P 52 HIS cc_start: 0.7748 (t-90) cc_final: 0.7332 (t-90) REVERT: P 60 ASN cc_start: 0.9280 (t0) cc_final: 0.8861 (t0) REVERT: P 111 MET cc_start: 0.8364 (mtm) cc_final: 0.8096 (mtt) outliers start: 4 outliers final: 0 residues processed: 606 average time/residue: 0.1470 time to fit residues: 134.5400 Evaluate side-chains 479 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 8.9990 chunk 170 optimal weight: 0.4980 chunk 102 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS H 82 GLN ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 567 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN N 77 GLN B 255 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 GLN C 255 GLN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.103490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.073399 restraints weight = 54711.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075634 restraints weight = 30432.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.077074 restraints weight = 21431.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.077922 restraints weight = 17378.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078448 restraints weight = 15405.620| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 19314 Z= 0.277 Angle : 0.773 11.497 26295 Z= 0.384 Chirality : 0.049 0.339 2952 Planarity : 0.004 0.038 3315 Dihedral : 5.758 23.290 2592 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.21 (0.17), residues: 2340 helix: 0.52 (0.38), residues: 180 sheet: -0.69 (0.17), residues: 867 loop : -1.03 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 61 TYR 0.041 0.002 TYR I 114 PHE 0.022 0.002 PHE E 582 TRP 0.018 0.002 TRP O 114 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.28 (19266) covalent geometry : angle 0.74539 / 0.38 (26172) SS BOND : bond 0.00640 / 0.40 ( 21) SS BOND : angle 1.69219 / 1.09 ( 42) hydrogen bonds : bond 0.03881 / 2.67 ( 622) hydrogen bonds : angle 6.17695 / 4.28 ( 1749) link_ALPHA1-3 : bond 0.00319 / 0.16 ( 3) link_ALPHA1-3 : angle 1.32549 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00097 / 0.05 ( 3) link_ALPHA1-6 : angle 1.80020 / 0.99 ( 9) link_BETA1-4 : bond 0.00418 / 0.21 ( 6) link_BETA1-4 : angle 2.77340 / 1.76 ( 18) link_NAG-ASN : bond 0.00381 / 0.25 ( 15) link_NAG-ASN : angle 4.37018 / 2.62 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9277 (mt0) cc_final: 0.8621 (mt0) REVERT: A 78 ASP cc_start: 0.8362 (t0) cc_final: 0.8034 (t0) REVERT: A 117 ASP cc_start: 0.8569 (p0) cc_final: 0.8241 (p0) REVERT: H 52 ARG cc_start: 0.8906 (mtm-85) cc_final: 0.8431 (mtm-85) REVERT: H 59 PHE cc_start: 0.7151 (t80) cc_final: 0.6879 (t80) REVERT: H 86 LEU cc_start: 0.9150 (mt) cc_final: 0.8866 (mt) REVERT: H 114 TYR cc_start: 0.6453 (m-10) cc_final: 0.5881 (m-10) REVERT: H 115 TYR cc_start: 0.8806 (m-10) cc_final: 0.8516 (m-10) REVERT: K 81 GLU cc_start: 0.8623 (mp0) cc_final: 0.8355 (mp0) REVERT: K 82 ASP cc_start: 0.6840 (m-30) cc_final: 0.6447 (m-30) REVERT: D 512 ASN cc_start: 0.9249 (t0) cc_final: 0.8864 (t0) REVERT: D 565 THR cc_start: 0.9294 (p) cc_final: 0.8983 (t) REVERT: Q 43 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7867 (mm-40) REVERT: N 15 SER cc_start: 0.8647 (m) cc_final: 0.8307 (p) REVERT: B 47 ASP cc_start: 0.6569 (t0) cc_final: 0.6183 (t0) REVERT: B 62 GLN cc_start: 0.9156 (mt0) cc_final: 0.8564 (mt0) REVERT: B 117 ASP cc_start: 0.8656 (p0) cc_final: 0.8407 (p0) REVERT: B 272 LYS cc_start: 0.4696 (pttt) cc_final: 0.4157 (ttmm) REVERT: I 46 GLU cc_start: 0.8691 (pt0) cc_final: 0.8235 (pm20) REVERT: I 59 PHE cc_start: 0.7236 (t80) cc_final: 0.6708 (t80) REVERT: I 76 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8461 (ptpp) REVERT: I 80 TYR cc_start: 0.8218 (m-80) cc_final: 0.7199 (m-80) REVERT: I 83 MET cc_start: 0.8632 (mmm) cc_final: 0.8027 (mmp) REVERT: I 86 LEU cc_start: 0.9171 (mt) cc_final: 0.8925 (mt) REVERT: L 31 ASN cc_start: 0.7291 (p0) cc_final: 0.6774 (m-40) REVERT: L 73 LEU cc_start: 0.8393 (tp) cc_final: 0.8030 (tp) REVERT: E 532 ILE cc_start: 0.9267 (mt) cc_final: 0.9010 (pt) REVERT: E 555 ILE cc_start: 0.9282 (mt) cc_final: 0.8979 (mt) REVERT: E 565 THR cc_start: 0.9283 (p) cc_final: 0.8912 (t) REVERT: E 581 THR cc_start: 0.9613 (m) cc_final: 0.9240 (p) REVERT: R 61 ASP cc_start: 0.8357 (p0) cc_final: 0.7954 (t0) REVERT: R 96 LEU cc_start: 0.9465 (mt) cc_final: 0.9244 (mt) REVERT: R 106 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7455 (tm-30) REVERT: O 16 GLU cc_start: 0.8635 (pt0) cc_final: 0.8232 (pt0) REVERT: C 62 GLN cc_start: 0.9109 (mt0) cc_final: 0.8584 (mt0) REVERT: C 117 ASP cc_start: 0.8615 (p0) cc_final: 0.8391 (p0) REVERT: J 12 VAL cc_start: 0.6873 (t) cc_final: 0.6580 (t) REVERT: J 43 LYS cc_start: 0.8518 (mppt) cc_final: 0.8126 (mppt) REVERT: J 46 GLU cc_start: 0.8816 (pt0) cc_final: 0.8314 (pm20) REVERT: J 57 LYS cc_start: 0.9171 (tptp) cc_final: 0.8855 (ttpt) REVERT: J 64 VAL cc_start: 0.9121 (m) cc_final: 0.8433 (t) REVERT: J 86 LEU cc_start: 0.9140 (mt) cc_final: 0.8814 (mt) REVERT: J 102 GLN cc_start: 0.8338 (mt0) cc_final: 0.7418 (mt0) REVERT: J 114 TYR cc_start: 0.6108 (m-10) cc_final: 0.5742 (m-10) REVERT: J 128 THR cc_start: 0.9377 (m) cc_final: 0.9172 (t) REVERT: M 55 GLN cc_start: 0.7578 (tm-30) cc_final: 0.7236 (tm-30) REVERT: M 73 LEU cc_start: 0.8034 (tp) cc_final: 0.7561 (tp) REVERT: M 90 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7505 (tp40) REVERT: F 581 THR cc_start: 0.9658 (m) cc_final: 0.9306 (p) REVERT: F 592 PHE cc_start: 0.8295 (t80) cc_final: 0.7896 (t80) REVERT: S 4 LEU cc_start: 0.8436 (mt) cc_final: 0.8134 (mt) REVERT: P 45 LEU cc_start: 0.8753 (mt) cc_final: 0.8447 (mt) REVERT: P 60 ASN cc_start: 0.9293 (t0) cc_final: 0.8911 (t0) REVERT: P 111 MET cc_start: 0.8590 (mtm) cc_final: 0.8203 (mtp) outliers start: 0 outliers final: 0 residues processed: 547 average time/residue: 0.1412 time to fit residues: 117.4057 Evaluate side-chains 434 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 95 optimal weight: 0.0170 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN N 77 GLN B 255 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.106568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076473 restraints weight = 53936.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078859 restraints weight = 29341.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.080407 restraints weight = 20262.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.081319 restraints weight = 16212.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.081832 restraints weight = 14288.095| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19314 Z= 0.144 Angle : 0.683 10.133 26295 Z= 0.342 Chirality : 0.047 0.320 2952 Planarity : 0.004 0.043 3315 Dihedral : 5.395 22.769 2592 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -0.94 (0.17), residues: 2340 helix: 0.48 (0.37), residues: 201 sheet: -0.41 (0.18), residues: 840 loop : -0.90 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 61 TYR 0.035 0.002 TYR I 114 PHE 0.025 0.002 PHE Q 34 TRP 0.013 0.001 TRP O 114 HIS 0.006 0.001 HIS I 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (19266) covalent geometry : angle 0.65845 / 0.34 (26172) SS BOND : bond 0.00503 / 0.31 ( 21) SS BOND : angle 1.38034 / 0.91 ( 42) hydrogen bonds : bond 0.03387 / 2.31 ( 622) hydrogen bonds : angle 5.83971 / 4.05 ( 1749) link_ALPHA1-3 : bond 0.00308 / 0.16 ( 3) link_ALPHA1-3 : angle 1.32711 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00296 / 0.15 ( 3) link_ALPHA1-6 : angle 1.44680 / 0.82 ( 9) link_BETA1-4 : bond 0.00411 / 0.23 ( 6) link_BETA1-4 : angle 2.67094 / 1.71 ( 18) link_NAG-ASN : bond 0.00493 / 0.34 ( 15) link_NAG-ASN : angle 3.88752 / 2.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9270 (mt0) cc_final: 0.8963 (mt0) REVERT: A 78 ASP cc_start: 0.8339 (t0) cc_final: 0.7969 (t0) REVERT: A 117 ASP cc_start: 0.8519 (p0) cc_final: 0.8188 (p0) REVERT: A 272 LYS cc_start: 0.4557 (pttt) cc_final: 0.4247 (pttm) REVERT: H 114 TYR cc_start: 0.6373 (m-10) cc_final: 0.5763 (m-10) REVERT: H 115 TYR cc_start: 0.8798 (m-10) cc_final: 0.8558 (m-10) REVERT: K 81 GLU cc_start: 0.8654 (mp0) cc_final: 0.8383 (mp0) REVERT: K 106 ILE cc_start: 0.3767 (tp) cc_final: 0.2979 (mm) REVERT: D 512 ASN cc_start: 0.9111 (t0) cc_final: 0.8700 (t0) REVERT: D 560 GLN cc_start: 0.9234 (tp40) cc_final: 0.8134 (tp40) REVERT: D 565 THR cc_start: 0.9252 (p) cc_final: 0.8910 (t) REVERT: D 581 THR cc_start: 0.9591 (t) cc_final: 0.9377 (p) REVERT: Q 17 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8027 (mt-10) REVERT: Q 34 PHE cc_start: 0.7490 (m-10) cc_final: 0.6926 (m-10) REVERT: Q 43 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7815 (mm-40) REVERT: N 15 SER cc_start: 0.8612 (m) cc_final: 0.8269 (p) REVERT: N 52 HIS cc_start: 0.7870 (t-90) cc_final: 0.7112 (t-90) REVERT: B 47 ASP cc_start: 0.6520 (t0) cc_final: 0.6105 (t0) REVERT: B 62 GLN cc_start: 0.9185 (mt0) cc_final: 0.8476 (mt0) REVERT: B 117 ASP cc_start: 0.8516 (p0) cc_final: 0.8260 (p0) REVERT: I 46 GLU cc_start: 0.8630 (pt0) cc_final: 0.8192 (pm20) REVERT: I 59 PHE cc_start: 0.7341 (t80) cc_final: 0.6764 (t80) REVERT: I 76 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8502 (ptpp) REVERT: I 80 TYR cc_start: 0.8173 (m-80) cc_final: 0.7287 (m-80) REVERT: I 83 MET cc_start: 0.8650 (mmm) cc_final: 0.8079 (mmp) REVERT: I 86 LEU cc_start: 0.9134 (mt) cc_final: 0.8888 (mt) REVERT: L 31 ASN cc_start: 0.7132 (p0) cc_final: 0.6772 (m-40) REVERT: L 55 GLN cc_start: 0.7147 (tm-30) cc_final: 0.6929 (tm-30) REVERT: L 70 ASP cc_start: 0.7219 (t0) cc_final: 0.6745 (p0) REVERT: L 73 LEU cc_start: 0.8379 (tp) cc_final: 0.7972 (tp) REVERT: E 514 ASN cc_start: 0.9146 (m-40) cc_final: 0.8736 (m-40) REVERT: E 555 ILE cc_start: 0.9129 (mt) cc_final: 0.8828 (mt) REVERT: E 560 GLN cc_start: 0.9173 (tp40) cc_final: 0.8198 (tp40) REVERT: E 565 THR cc_start: 0.9254 (p) cc_final: 0.8902 (t) REVERT: E 579 LEU cc_start: 0.9132 (mm) cc_final: 0.8780 (tp) REVERT: E 581 THR cc_start: 0.9618 (m) cc_final: 0.9296 (p) REVERT: E 591 ASP cc_start: 0.9102 (t0) cc_final: 0.8895 (t0) REVERT: R 61 ASP cc_start: 0.8289 (p0) cc_final: 0.7871 (t0) REVERT: R 82 GLU cc_start: 0.8170 (pm20) cc_final: 0.7599 (pm20) REVERT: R 96 LEU cc_start: 0.9416 (mt) cc_final: 0.9033 (tt) REVERT: R 106 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7402 (tm-30) REVERT: C 62 GLN cc_start: 0.9050 (mt0) cc_final: 0.8505 (mt0) REVERT: C 68 LEU cc_start: 0.9376 (mt) cc_final: 0.9017 (mt) REVERT: J 12 VAL cc_start: 0.6881 (t) cc_final: 0.6614 (t) REVERT: J 43 LYS cc_start: 0.8523 (mppt) cc_final: 0.8140 (mppt) REVERT: J 46 GLU cc_start: 0.8840 (pt0) cc_final: 0.8284 (pm20) REVERT: J 57 LYS cc_start: 0.9134 (tptp) cc_final: 0.8860 (ttpt) REVERT: J 86 LEU cc_start: 0.8985 (mt) cc_final: 0.8741 (mt) REVERT: J 101 LEU cc_start: 0.9004 (tp) cc_final: 0.8780 (tp) REVERT: J 102 GLN cc_start: 0.8211 (mt0) cc_final: 0.7800 (mt0) REVERT: J 115 TYR cc_start: 0.8770 (m-10) cc_final: 0.8482 (m-10) REVERT: M 24 ARG cc_start: 0.7248 (mmm-85) cc_final: 0.6902 (mmm-85) REVERT: M 55 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7260 (tm-30) REVERT: M 73 LEU cc_start: 0.7951 (tp) cc_final: 0.7441 (tp) REVERT: M 79 GLN cc_start: 0.3943 (pm20) cc_final: 0.3210 (pm20) REVERT: F 592 PHE cc_start: 0.8276 (t80) cc_final: 0.8007 (t80) REVERT: S 4 LEU cc_start: 0.8397 (mt) cc_final: 0.8170 (mt) REVERT: S 78 ARG cc_start: 0.8457 (ttp-170) cc_final: 0.7888 (ttp-170) REVERT: S 96 LEU cc_start: 0.9475 (mp) cc_final: 0.9127 (tt) REVERT: P 45 LEU cc_start: 0.8734 (mt) cc_final: 0.8511 (mt) REVERT: P 60 ASN cc_start: 0.9268 (t0) cc_final: 0.8862 (t0) REVERT: P 111 MET cc_start: 0.8287 (mtm) cc_final: 0.7874 (mtt) outliers start: 0 outliers final: 0 residues processed: 583 average time/residue: 0.1375 time to fit residues: 122.6560 Evaluate side-chains 461 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 3 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 139 HIS A 255 GLN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN N 77 GLN B 255 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 GLN E 521 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN C 139 HIS ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS J 82 GLN ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN P 76 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.102665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072307 restraints weight = 55000.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.074543 restraints weight = 30898.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075976 restraints weight = 21736.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.076814 restraints weight = 17684.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.077358 restraints weight = 15651.773| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 19314 Z= 0.328 Angle : 0.824 11.732 26295 Z= 0.411 Chirality : 0.050 0.344 2952 Planarity : 0.005 0.063 3315 Dihedral : 5.809 24.616 2592 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.28 (0.17), residues: 2340 helix: 0.57 (0.38), residues: 183 sheet: -0.90 (0.17), residues: 924 loop : -0.94 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 24 TYR 0.038 0.003 TYR I 114 PHE 0.039 0.003 PHE Q 34 TRP 0.020 0.002 TRP O 114 HIS 0.012 0.002 HIS P 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.33 (19266) covalent geometry : angle 0.79712 / 0.40 (26172) SS BOND : bond 0.00769 / 0.46 ( 21) SS BOND : angle 1.94518 / 1.30 ( 42) hydrogen bonds : bond 0.04046 / 2.78 ( 622) hydrogen bonds : angle 6.24601 / 4.31 ( 1749) link_ALPHA1-3 : bond 0.00322 / 0.17 ( 3) link_ALPHA1-3 : angle 1.37472 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00071 / 0.04 ( 3) link_ALPHA1-6 : angle 1.87105 / 1.03 ( 9) link_BETA1-4 : bond 0.00503 / 0.28 ( 6) link_BETA1-4 : angle 2.96571 / 1.89 ( 18) link_NAG-ASN : bond 0.00413 / 0.26 ( 15) link_NAG-ASN : angle 4.40536 / 2.67 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9191 (mt0) cc_final: 0.8896 (mt0) REVERT: A 103 GLU cc_start: 0.8422 (tt0) cc_final: 0.8212 (tt0) REVERT: A 117 ASP cc_start: 0.8627 (p0) cc_final: 0.8343 (p0) REVERT: H 52 ARG cc_start: 0.8939 (mtm-85) cc_final: 0.8440 (mtm-85) REVERT: H 87 ARG cc_start: 0.8315 (mmp80) cc_final: 0.8100 (mmp80) REVERT: H 114 TYR cc_start: 0.6496 (m-10) cc_final: 0.5855 (m-10) REVERT: H 115 TYR cc_start: 0.8875 (m-10) cc_final: 0.8576 (m-10) REVERT: K 81 GLU cc_start: 0.8680 (mp0) cc_final: 0.8471 (mp0) REVERT: D 512 ASN cc_start: 0.9196 (t0) cc_final: 0.8783 (t0) REVERT: D 560 GLN cc_start: 0.9306 (tp40) cc_final: 0.8338 (tp40) REVERT: D 592 PHE cc_start: 0.8426 (t80) cc_final: 0.7996 (t80) REVERT: Q 17 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7948 (mt-10) REVERT: Q 34 PHE cc_start: 0.8103 (m-10) cc_final: 0.7878 (m-10) REVERT: Q 43 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7769 (mm-40) REVERT: Q 61 ASP cc_start: 0.8138 (p0) cc_final: 0.7723 (p0) REVERT: N 15 SER cc_start: 0.8560 (m) cc_final: 0.7418 (p) REVERT: B 47 ASP cc_start: 0.6350 (t0) cc_final: 0.5889 (t0) REVERT: B 62 GLN cc_start: 0.9118 (mt0) cc_final: 0.8593 (mt0) REVERT: B 117 ASP cc_start: 0.8656 (p0) cc_final: 0.8442 (p0) REVERT: I 46 GLU cc_start: 0.8728 (pt0) cc_final: 0.8244 (pm20) REVERT: I 48 MET cc_start: 0.8366 (mmm) cc_final: 0.7998 (tpp) REVERT: I 59 PHE cc_start: 0.7530 (t80) cc_final: 0.6859 (t80) REVERT: I 80 TYR cc_start: 0.8229 (m-80) cc_final: 0.7365 (m-80) REVERT: I 83 MET cc_start: 0.8652 (mmm) cc_final: 0.8021 (mmp) REVERT: L 31 ASN cc_start: 0.7328 (p0) cc_final: 0.6801 (m-40) REVERT: L 55 GLN cc_start: 0.7486 (tm-30) cc_final: 0.7204 (tm-30) REVERT: L 69 THR cc_start: 0.8505 (p) cc_final: 0.8287 (p) REVERT: L 73 LEU cc_start: 0.8308 (tp) cc_final: 0.7913 (tp) REVERT: L 104 LEU cc_start: 0.7868 (tp) cc_final: 0.7600 (tt) REVERT: E 532 ILE cc_start: 0.9335 (mt) cc_final: 0.9099 (pt) REVERT: E 555 ILE cc_start: 0.9337 (mt) cc_final: 0.9048 (mt) REVERT: E 564 GLU cc_start: 0.8029 (mp0) cc_final: 0.7677 (mp0) REVERT: E 565 THR cc_start: 0.9243 (p) cc_final: 0.8874 (t) REVERT: E 581 THR cc_start: 0.9609 (m) cc_final: 0.9245 (p) REVERT: E 592 PHE cc_start: 0.8375 (t80) cc_final: 0.7935 (t80) REVERT: E 597 TRP cc_start: 0.7639 (t-100) cc_final: 0.7181 (t-100) REVERT: R 61 ASP cc_start: 0.8385 (p0) cc_final: 0.7947 (t0) REVERT: R 76 ILE cc_start: 0.9329 (mp) cc_final: 0.9032 (tt) REVERT: R 96 LEU cc_start: 0.9455 (mt) cc_final: 0.9232 (mt) REVERT: R 106 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7429 (tm-30) REVERT: O 16 GLU cc_start: 0.8588 (pt0) cc_final: 0.8174 (pt0) REVERT: C 62 GLN cc_start: 0.9202 (mt0) cc_final: 0.8661 (mt0) REVERT: J 12 VAL cc_start: 0.6759 (t) cc_final: 0.6444 (t) REVERT: J 35 HIS cc_start: 0.8285 (m-70) cc_final: 0.8033 (m90) REVERT: J 46 GLU cc_start: 0.8932 (pt0) cc_final: 0.8331 (pm20) REVERT: J 57 LYS cc_start: 0.9164 (tptp) cc_final: 0.8838 (ttpt) REVERT: J 86 LEU cc_start: 0.9034 (mt) cc_final: 0.8754 (mt) REVERT: J 101 LEU cc_start: 0.9171 (tp) cc_final: 0.8926 (tp) REVERT: J 102 GLN cc_start: 0.8244 (mt0) cc_final: 0.7476 (mt0) REVERT: J 114 TYR cc_start: 0.6436 (m-10) cc_final: 0.5630 (m-10) REVERT: M 24 ARG cc_start: 0.7420 (mmm-85) cc_final: 0.7078 (mmm-85) REVERT: M 55 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7244 (tm-30) REVERT: M 69 THR cc_start: 0.8462 (p) cc_final: 0.8253 (p) REVERT: M 73 LEU cc_start: 0.8087 (tp) cc_final: 0.7579 (tp) REVERT: S 4 LEU cc_start: 0.8463 (mt) cc_final: 0.8190 (mt) REVERT: S 78 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8125 (ttp-170) REVERT: P 60 ASN cc_start: 0.9329 (t0) cc_final: 0.9033 (t0) REVERT: P 111 MET cc_start: 0.8518 (mtm) cc_final: 0.8217 (mtp) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.1355 time to fit residues: 109.5868 Evaluate side-chains 433 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 103 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN N 77 GLN B 255 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 GLN ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.106295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076160 restraints weight = 53881.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.078528 restraints weight = 29640.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.080030 restraints weight = 20636.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080942 restraints weight = 16628.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.081453 restraints weight = 14653.594| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19314 Z= 0.140 Angle : 0.719 10.513 26295 Z= 0.359 Chirality : 0.048 0.311 2952 Planarity : 0.004 0.055 3315 Dihedral : 5.453 22.328 2592 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -0.95 (0.17), residues: 2340 helix: 0.63 (0.37), residues: 201 sheet: -0.56 (0.17), residues: 870 loop : -0.82 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 18 TYR 0.033 0.002 TYR I 114 PHE 0.034 0.002 PHE Q 34 TRP 0.013 0.001 TRP B 275 HIS 0.009 0.001 HIS P 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (19266) covalent geometry : angle 0.69417 / 0.35 (26172) SS BOND : bond 0.00527 / 0.28 ( 21) SS BOND : angle 1.56893 / 1.00 ( 42) hydrogen bonds : bond 0.03458 / 2.35 ( 622) hydrogen bonds : angle 5.84523 / 4.04 ( 1749) link_ALPHA1-3 : bond 0.00309 / 0.15 ( 3) link_ALPHA1-3 : angle 1.41890 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00378 / 0.19 ( 3) link_ALPHA1-6 : angle 1.41048 / 0.80 ( 9) link_BETA1-4 : bond 0.00458 / 0.25 ( 6) link_BETA1-4 : angle 2.75903 / 1.75 ( 18) link_NAG-ASN : bond 0.00607 / 0.44 ( 15) link_NAG-ASN : angle 3.92514 / 2.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7645 (mmpt) cc_final: 0.7289 (mmmt) REVERT: A 62 GLN cc_start: 0.8987 (mt0) cc_final: 0.8551 (mt0) REVERT: A 117 ASP cc_start: 0.8573 (p0) cc_final: 0.8370 (p0) REVERT: A 272 LYS cc_start: 0.4861 (pttt) cc_final: 0.4561 (pttm) REVERT: H 50 PHE cc_start: 0.6882 (p90) cc_final: 0.6582 (p90) REVERT: H 59 PHE cc_start: 0.7036 (t80) cc_final: 0.6811 (t80) REVERT: H 86 LEU cc_start: 0.9103 (mt) cc_final: 0.8836 (mt) REVERT: H 114 TYR cc_start: 0.6247 (m-10) cc_final: 0.5652 (m-10) REVERT: D 512 ASN cc_start: 0.9087 (t0) cc_final: 0.8779 (t0) REVERT: D 560 GLN cc_start: 0.9173 (tp40) cc_final: 0.8188 (tp40) REVERT: D 565 THR cc_start: 0.9280 (p) cc_final: 0.8996 (t) REVERT: D 592 PHE cc_start: 0.8346 (t80) cc_final: 0.8056 (t80) REVERT: Q 43 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7748 (mm-40) REVERT: N 15 SER cc_start: 0.8653 (m) cc_final: 0.8303 (p) REVERT: B 47 ASP cc_start: 0.6617 (t0) cc_final: 0.6077 (t0) REVERT: B 62 GLN cc_start: 0.9077 (mt0) cc_final: 0.8580 (mt0) REVERT: B 117 ASP cc_start: 0.8618 (p0) cc_final: 0.8391 (p0) REVERT: I 46 GLU cc_start: 0.8692 (pt0) cc_final: 0.8205 (pm20) REVERT: I 48 MET cc_start: 0.8322 (mmm) cc_final: 0.8025 (tpp) REVERT: I 59 PHE cc_start: 0.7351 (t80) cc_final: 0.6689 (t80) REVERT: I 80 TYR cc_start: 0.8157 (m-80) cc_final: 0.7742 (m-80) REVERT: I 83 MET cc_start: 0.8643 (mmm) cc_final: 0.7815 (mmp) REVERT: L 31 ASN cc_start: 0.7094 (p0) cc_final: 0.6658 (m-40) REVERT: L 55 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7247 (tm-30) REVERT: L 70 ASP cc_start: 0.7169 (t0) cc_final: 0.6764 (p0) REVERT: L 73 LEU cc_start: 0.8367 (tp) cc_final: 0.7938 (tp) REVERT: L 104 LEU cc_start: 0.7712 (tp) cc_final: 0.7425 (tt) REVERT: E 514 ASN cc_start: 0.9187 (m-40) cc_final: 0.8746 (m-40) REVERT: E 555 ILE cc_start: 0.9214 (mt) cc_final: 0.8899 (mt) REVERT: E 560 GLN cc_start: 0.8879 (tp40) cc_final: 0.7794 (tp40) REVERT: E 564 GLU cc_start: 0.7765 (mp0) cc_final: 0.7264 (mp0) REVERT: E 565 THR cc_start: 0.9180 (p) cc_final: 0.8821 (t) REVERT: E 579 LEU cc_start: 0.9152 (mm) cc_final: 0.8821 (tp) REVERT: E 581 THR cc_start: 0.9585 (m) cc_final: 0.9283 (p) REVERT: E 592 PHE cc_start: 0.8396 (t80) cc_final: 0.7945 (t80) REVERT: E 597 TRP cc_start: 0.7249 (t-100) cc_final: 0.6865 (t-100) REVERT: R 18 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7701 (ttp80) REVERT: R 61 ASP cc_start: 0.8312 (p0) cc_final: 0.7836 (t0) REVERT: R 82 GLU cc_start: 0.8172 (pm20) cc_final: 0.7670 (pm20) REVERT: R 96 LEU cc_start: 0.9409 (mt) cc_final: 0.9049 (tt) REVERT: R 106 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7397 (tm-30) REVERT: O 16 GLU cc_start: 0.8536 (pt0) cc_final: 0.8207 (pt0) REVERT: C 62 GLN cc_start: 0.9086 (mt0) cc_final: 0.8490 (mt0) REVERT: C 68 LEU cc_start: 0.9379 (mt) cc_final: 0.9017 (mt) REVERT: J 12 VAL cc_start: 0.6754 (t) cc_final: 0.6488 (t) REVERT: J 46 GLU cc_start: 0.8898 (pt0) cc_final: 0.8390 (pm20) REVERT: J 57 LYS cc_start: 0.9098 (tptp) cc_final: 0.8856 (ttpt) REVERT: J 86 LEU cc_start: 0.8972 (mt) cc_final: 0.8725 (mt) REVERT: J 102 GLN cc_start: 0.8132 (mt0) cc_final: 0.7301 (mt0) REVERT: J 114 TYR cc_start: 0.6334 (m-10) cc_final: 0.5545 (m-10) REVERT: J 115 TYR cc_start: 0.8872 (m-10) cc_final: 0.8536 (m-10) REVERT: M 24 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.7223 (mmm-85) REVERT: M 55 GLN cc_start: 0.7705 (tm-30) cc_final: 0.7307 (tm-30) REVERT: M 69 THR cc_start: 0.8348 (p) cc_final: 0.8091 (p) REVERT: M 73 LEU cc_start: 0.8029 (tp) cc_final: 0.7486 (tp) REVERT: F 560 GLN cc_start: 0.9140 (tp40) cc_final: 0.7921 (tp40) REVERT: S 4 LEU cc_start: 0.8382 (mt) cc_final: 0.8124 (mt) REVERT: P 60 ASN cc_start: 0.9288 (t0) cc_final: 0.8963 (t0) outliers start: 0 outliers final: 0 residues processed: 551 average time/residue: 0.1378 time to fit residues: 117.1740 Evaluate side-chains 457 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.0030 chunk 148 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 175 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN N 76 ASN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN J 74 ASN ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.107853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.077803 restraints weight = 53637.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080176 restraints weight = 29163.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.081783 restraints weight = 20141.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.082709 restraints weight = 16095.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.083197 restraints weight = 14132.966| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19314 Z= 0.126 Angle : 0.700 11.045 26295 Z= 0.348 Chirality : 0.047 0.289 2952 Planarity : 0.004 0.051 3315 Dihedral : 5.231 22.926 2592 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -0.75 (0.18), residues: 2340 helix: 0.79 (0.38), residues: 198 sheet: -0.33 (0.17), residues: 837 loop : -0.77 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 18 TYR 0.029 0.002 TYR I 114 PHE 0.028 0.001 PHE Q 72 TRP 0.012 0.001 TRP R 36 HIS 0.010 0.001 HIS H 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (19266) covalent geometry : angle 0.67755 / 0.34 (26172) SS BOND : bond 0.00472 / 0.28 ( 21) SS BOND : angle 1.43995 / 0.88 ( 42) hydrogen bonds : bond 0.03281 / 2.25 ( 622) hydrogen bonds : angle 5.57569 / 3.85 ( 1749) link_ALPHA1-3 : bond 0.00401 / 0.20 ( 3) link_ALPHA1-3 : angle 1.46788 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00559 / 0.27 ( 3) link_ALPHA1-6 : angle 1.49685 / 0.85 ( 9) link_BETA1-4 : bond 0.00740 / 0.46 ( 6) link_BETA1-4 : angle 2.79622 / 1.75 ( 18) link_NAG-ASN : bond 0.00557 / 0.40 ( 15) link_NAG-ASN : angle 3.67588 / 2.20 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9029 (mt0) cc_final: 0.8358 (mt0) REVERT: A 272 LYS cc_start: 0.4698 (pttt) cc_final: 0.4423 (pttm) REVERT: H 50 PHE cc_start: 0.6616 (p90) cc_final: 0.6402 (p90) REVERT: H 73 ASP cc_start: 0.8659 (t0) cc_final: 0.8114 (p0) REVERT: H 114 TYR cc_start: 0.6332 (m-10) cc_final: 0.5815 (m-10) REVERT: K 58 VAL cc_start: 0.8171 (p) cc_final: 0.7958 (t) REVERT: K 106 ILE cc_start: 0.3626 (tp) cc_final: 0.2947 (mm) REVERT: D 512 ASN cc_start: 0.8975 (t0) cc_final: 0.8772 (t0) REVERT: D 560 GLN cc_start: 0.9128 (tp40) cc_final: 0.8664 (tm-30) REVERT: D 565 THR cc_start: 0.9288 (p) cc_final: 0.8982 (t) REVERT: D 592 PHE cc_start: 0.8342 (t80) cc_final: 0.7882 (t80) REVERT: Q 43 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7843 (mm-40) REVERT: N 15 SER cc_start: 0.8568 (m) cc_final: 0.7385 (p) REVERT: N 52 HIS cc_start: 0.7917 (t-90) cc_final: 0.7537 (t70) REVERT: B 47 ASP cc_start: 0.6605 (t0) cc_final: 0.6056 (t0) REVERT: B 62 GLN cc_start: 0.9160 (mt0) cc_final: 0.8721 (mt0) REVERT: B 117 ASP cc_start: 0.8616 (p0) cc_final: 0.8382 (p0) REVERT: I 46 GLU cc_start: 0.8677 (pt0) cc_final: 0.8222 (pm20) REVERT: I 59 PHE cc_start: 0.7284 (t80) cc_final: 0.6831 (t80) REVERT: I 80 TYR cc_start: 0.8261 (m-80) cc_final: 0.7858 (m-80) REVERT: I 83 MET cc_start: 0.8712 (mmm) cc_final: 0.7915 (mmm) REVERT: L 31 ASN cc_start: 0.7117 (p0) cc_final: 0.6909 (m-40) REVERT: L 55 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7228 (tm-30) REVERT: L 70 ASP cc_start: 0.7228 (t0) cc_final: 0.6811 (p0) REVERT: L 73 LEU cc_start: 0.8343 (tp) cc_final: 0.7903 (tp) REVERT: L 104 LEU cc_start: 0.7653 (tp) cc_final: 0.7393 (tt) REVERT: E 514 ASN cc_start: 0.9124 (m-40) cc_final: 0.8525 (m-40) REVERT: E 555 ILE cc_start: 0.9170 (mt) cc_final: 0.8850 (mt) REVERT: E 560 GLN cc_start: 0.8886 (tp40) cc_final: 0.7635 (tp40) REVERT: E 564 GLU cc_start: 0.7744 (mp0) cc_final: 0.7400 (mp0) REVERT: E 565 THR cc_start: 0.9191 (p) cc_final: 0.8868 (t) REVERT: E 579 LEU cc_start: 0.9005 (mm) cc_final: 0.8758 (tp) REVERT: E 581 THR cc_start: 0.9561 (m) cc_final: 0.9273 (p) REVERT: R 61 ASP cc_start: 0.8282 (p0) cc_final: 0.7842 (t0) REVERT: R 76 ILE cc_start: 0.9302 (mp) cc_final: 0.9013 (tt) REVERT: R 96 LEU cc_start: 0.9376 (mt) cc_final: 0.9003 (tt) REVERT: O 16 GLU cc_start: 0.8379 (pt0) cc_final: 0.8047 (pt0) REVERT: C 62 GLN cc_start: 0.9048 (mt0) cc_final: 0.8507 (mt0) REVERT: J 12 VAL cc_start: 0.6779 (t) cc_final: 0.6508 (t) REVERT: J 46 GLU cc_start: 0.8879 (pt0) cc_final: 0.8294 (pm20) REVERT: J 57 LYS cc_start: 0.9050 (tptp) cc_final: 0.8702 (tttt) REVERT: J 70 ILE cc_start: 0.7994 (tt) cc_final: 0.7773 (tp) REVERT: J 102 GLN cc_start: 0.8077 (mt0) cc_final: 0.7186 (mt0) REVERT: J 114 TYR cc_start: 0.6272 (m-10) cc_final: 0.5567 (m-10) REVERT: J 115 TYR cc_start: 0.8832 (m-10) cc_final: 0.8558 (m-10) REVERT: M 24 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7123 (mmm-85) REVERT: M 55 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7430 (tm-30) REVERT: M 70 ASP cc_start: 0.7609 (t0) cc_final: 0.7068 (p0) REVERT: M 73 LEU cc_start: 0.7954 (tp) cc_final: 0.7443 (tp) REVERT: M 79 GLN cc_start: 0.3695 (pm20) cc_final: 0.2945 (pm20) REVERT: F 560 GLN cc_start: 0.8890 (tp40) cc_final: 0.7839 (tp40) REVERT: F 564 GLU cc_start: 0.8045 (mp0) cc_final: 0.7625 (mp0) REVERT: F 578 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8299 (mm-30) REVERT: S 4 LEU cc_start: 0.8391 (mt) cc_final: 0.8132 (mt) REVERT: S 96 LEU cc_start: 0.9404 (mp) cc_final: 0.9146 (tt) REVERT: P 1 GLN cc_start: 0.6701 (mm-40) cc_final: 0.6394 (mm-40) REVERT: P 60 ASN cc_start: 0.9260 (t0) cc_final: 0.8914 (t0) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 0.1367 time to fit residues: 119.4477 Evaluate side-chains 461 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 104 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 22 optimal weight: 0.0040 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Q 39 GLN N 76 ASN N 77 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.107257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.077132 restraints weight = 54292.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.079447 restraints weight = 29618.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080973 restraints weight = 20654.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.081868 restraints weight = 16687.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.082422 restraints weight = 14725.901| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19314 Z= 0.143 Angle : 0.710 11.861 26295 Z= 0.353 Chirality : 0.047 0.291 2952 Planarity : 0.005 0.079 3315 Dihedral : 5.237 24.990 2592 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -0.75 (0.18), residues: 2340 helix: 0.70 (0.36), residues: 201 sheet: -0.35 (0.17), residues: 870 loop : -0.74 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 18 TYR 0.019 0.002 TYR I 114 PHE 0.021 0.001 PHE F 592 TRP 0.014 0.001 TRP O 114 HIS 0.012 0.001 HIS O 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (19266) covalent geometry : angle 0.68846 / 0.35 (26172) SS BOND : bond 0.00487 / 0.30 ( 21) SS BOND : angle 1.64849 / 1.06 ( 42) hydrogen bonds : bond 0.03310 / 2.23 ( 622) hydrogen bonds : angle 5.49932 / 3.79 ( 1749) link_ALPHA1-3 : bond 0.00315 / 0.16 ( 3) link_ALPHA1-3 : angle 1.43499 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00333 / 0.17 ( 3) link_ALPHA1-6 : angle 1.49629 / 0.84 ( 9) link_BETA1-4 : bond 0.00505 / 0.27 ( 6) link_BETA1-4 : angle 2.70656 / 1.71 ( 18) link_NAG-ASN : bond 0.00562 / 0.40 ( 15) link_NAG-ASN : angle 3.57510 / 2.18 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9100 (mt0) cc_final: 0.8413 (mt0) REVERT: A 272 LYS cc_start: 0.4768 (pttt) cc_final: 0.4519 (pttm) REVERT: H 73 ASP cc_start: 0.8683 (t0) cc_final: 0.8158 (p0) REVERT: H 80 TYR cc_start: 0.8096 (m-80) cc_final: 0.7861 (m-80) REVERT: H 114 TYR cc_start: 0.6361 (m-10) cc_final: 0.5786 (m-10) REVERT: K 55 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7449 (tm-30) REVERT: K 58 VAL cc_start: 0.8084 (p) cc_final: 0.7680 (m) REVERT: K 69 THR cc_start: 0.8361 (p) cc_final: 0.7875 (p) REVERT: K 106 ILE cc_start: 0.3697 (tp) cc_final: 0.2967 (mm) REVERT: D 512 ASN cc_start: 0.9001 (t0) cc_final: 0.8773 (t0) REVERT: D 560 GLN cc_start: 0.9123 (tp40) cc_final: 0.8572 (tm-30) REVERT: D 565 THR cc_start: 0.9293 (p) cc_final: 0.9019 (t) REVERT: Q 34 PHE cc_start: 0.8123 (m-10) cc_final: 0.7592 (m-10) REVERT: Q 43 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7846 (mm-40) REVERT: N 15 SER cc_start: 0.8551 (m) cc_final: 0.7351 (p) REVERT: N 52 HIS cc_start: 0.7942 (t-90) cc_final: 0.7625 (t70) REVERT: B 47 ASP cc_start: 0.6745 (t0) cc_final: 0.6169 (t0) REVERT: B 62 GLN cc_start: 0.9204 (mt0) cc_final: 0.8681 (mt0) REVERT: B 117 ASP cc_start: 0.8645 (p0) cc_final: 0.8399 (p0) REVERT: I 46 GLU cc_start: 0.8684 (pt0) cc_final: 0.8227 (pm20) REVERT: I 59 PHE cc_start: 0.7370 (t80) cc_final: 0.6838 (t80) REVERT: I 80 TYR cc_start: 0.8229 (m-80) cc_final: 0.7878 (m-80) REVERT: I 83 MET cc_start: 0.8739 (mmm) cc_final: 0.7931 (mmm) REVERT: L 55 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7339 (tm-30) REVERT: L 70 ASP cc_start: 0.7135 (t0) cc_final: 0.6727 (p0) REVERT: L 73 LEU cc_start: 0.8310 (tp) cc_final: 0.7888 (tp) REVERT: L 104 LEU cc_start: 0.7635 (tp) cc_final: 0.7308 (tt) REVERT: E 514 ASN cc_start: 0.9064 (m-40) cc_final: 0.8601 (m-40) REVERT: E 555 ILE cc_start: 0.9161 (mt) cc_final: 0.8806 (mt) REVERT: E 560 GLN cc_start: 0.8879 (tp40) cc_final: 0.7627 (tp40) REVERT: E 564 GLU cc_start: 0.7721 (mp0) cc_final: 0.7451 (mp0) REVERT: E 565 THR cc_start: 0.9217 (p) cc_final: 0.8865 (t) REVERT: E 579 LEU cc_start: 0.9118 (mm) cc_final: 0.8829 (tp) REVERT: E 581 THR cc_start: 0.9567 (m) cc_final: 0.9278 (p) REVERT: E 597 TRP cc_start: 0.7320 (t-100) cc_final: 0.6977 (t-100) REVERT: R 18 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7477 (ttp80) REVERT: R 61 ASP cc_start: 0.8258 (p0) cc_final: 0.7838 (t0) REVERT: R 76 ILE cc_start: 0.9316 (mp) cc_final: 0.9037 (tt) REVERT: R 82 GLU cc_start: 0.8180 (pm20) cc_final: 0.7756 (pm20) REVERT: R 96 LEU cc_start: 0.9360 (mt) cc_final: 0.9022 (tt) REVERT: R 107 ILE cc_start: 0.6180 (tp) cc_final: 0.5798 (tt) REVERT: O 13 LYS cc_start: 0.8952 (tmmt) cc_final: 0.8508 (ttpp) REVERT: O 16 GLU cc_start: 0.8292 (pt0) cc_final: 0.7511 (pt0) REVERT: C 62 GLN cc_start: 0.9041 (mt0) cc_final: 0.8514 (mt0) REVERT: C 68 LEU cc_start: 0.9378 (mt) cc_final: 0.9065 (mt) REVERT: J 12 VAL cc_start: 0.6815 (t) cc_final: 0.6539 (t) REVERT: J 46 GLU cc_start: 0.8856 (pt0) cc_final: 0.8232 (pm20) REVERT: J 57 LYS cc_start: 0.9094 (tptp) cc_final: 0.8763 (tttt) REVERT: J 70 ILE cc_start: 0.8010 (tt) cc_final: 0.7791 (tp) REVERT: J 102 GLN cc_start: 0.8096 (mt0) cc_final: 0.7113 (mt0) REVERT: J 114 TYR cc_start: 0.6356 (m-10) cc_final: 0.5648 (m-10) REVERT: M 24 ARG cc_start: 0.7634 (mmm-85) cc_final: 0.7159 (mmm-85) REVERT: M 31 ASN cc_start: 0.8176 (t0) cc_final: 0.7911 (t0) REVERT: M 55 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7434 (tm-30) REVERT: M 70 ASP cc_start: 0.7583 (t0) cc_final: 0.7036 (p0) REVERT: M 73 LEU cc_start: 0.7982 (tp) cc_final: 0.7528 (tp) REVERT: F 560 GLN cc_start: 0.8921 (tp40) cc_final: 0.7949 (tp40) REVERT: F 564 GLU cc_start: 0.8073 (mp0) cc_final: 0.7651 (mp0) REVERT: S 4 LEU cc_start: 0.8422 (mt) cc_final: 0.8138 (mt) REVERT: S 96 LEU cc_start: 0.9398 (mp) cc_final: 0.9136 (tt) REVERT: P 1 GLN cc_start: 0.6723 (mm-40) cc_final: 0.6407 (mm-40) REVERT: P 18 LEU cc_start: 0.9016 (tp) cc_final: 0.8579 (mm) REVERT: P 60 ASN cc_start: 0.9281 (t0) cc_final: 0.8929 (t0) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.1331 time to fit residues: 112.5069 Evaluate side-chains 450 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 93 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN P 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.104017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.074277 restraints weight = 55015.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076946 restraints weight = 31178.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.077489 restraints weight = 19653.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077946 restraints weight = 18440.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.077878 restraints weight = 16772.200| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 19314 Z= 0.267 Angle : 0.789 10.853 26295 Z= 0.393 Chirality : 0.049 0.322 2952 Planarity : 0.005 0.072 3315 Dihedral : 5.547 25.093 2592 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -0.99 (0.18), residues: 2340 helix: 0.73 (0.37), residues: 183 sheet: -0.66 (0.17), residues: 903 loop : -0.79 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 18 TYR 0.026 0.003 TYR F 534 PHE 0.026 0.002 PHE F 582 TRP 0.022 0.002 TRP O 114 HIS 0.011 0.002 HIS O 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.27 (19266) covalent geometry : angle 0.76542 / 0.39 (26172) SS BOND : bond 0.00573 / 0.36 ( 21) SS BOND : angle 1.79663 / 1.16 ( 42) hydrogen bonds : bond 0.03696 / 2.51 ( 622) hydrogen bonds : angle 5.77167 / 3.97 ( 1749) link_ALPHA1-3 : bond 0.00195 / 0.10 ( 3) link_ALPHA1-3 : angle 1.42919 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00120 / 0.06 ( 3) link_ALPHA1-6 : angle 1.79170 / 1.00 ( 9) link_BETA1-4 : bond 0.00469 / 0.24 ( 6) link_BETA1-4 : angle 2.85124 / 1.80 ( 18) link_NAG-ASN : bond 0.00387 / 0.25 ( 15) link_NAG-ASN : angle 3.93127 / 2.41 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3885.98 seconds wall clock time: 67 minutes 53.41 seconds (4073.41 seconds total)