Starting phenix.real_space_refine on Thu Mar 5 03:44:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pci_20301/03_2026/6pci_20301.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pci_20301/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pci_20301/03_2026/6pci_20301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pci_20301/03_2026/6pci_20301.map" model { file = "/net/cci-nas-00/data/ceres_data/6pci_20301/03_2026/6pci_20301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pci_20301/03_2026/6pci_20301.cif" } 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-dev-5986/lib/python3.9/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 dihedrals: 15 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 dihedrals: 12 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: 3.22, per 1000 atoms: 0.17 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: 1.68 Conformation dependent library (CDL) restraints added in 687.3 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: 0.94 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: 4.08 Time building geometry restraints manager: 2.17 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 - 20.77: 11308 20.77 - 41.54: 266 41.54 - 62.31: 51 62.31 - 83.09: 18 83.09 - 103.86: 12 Dihedral angle restraints: 11655 sinusoidal: 4860 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 11652 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: 0.02 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.710 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 10.797 103.857 7278 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 covalent geometry : bond 0.00932 (19266) covalent geometry : angle 1.05240 (26172) SS BOND : bond 0.00793 ( 21) SS BOND : angle 1.88223 ( 42) hydrogen bonds : bond 0.26686 ( 622) hydrogen bonds : angle 10.66242 ( 1749) link_ALPHA1-3 : bond 0.00069 ( 3) link_ALPHA1-3 : angle 1.77423 ( 9) link_ALPHA1-6 : bond 0.00049 ( 3) link_ALPHA1-6 : angle 1.68010 ( 9) link_BETA1-4 : bond 0.00536 ( 6) link_BETA1-4 : angle 4.23777 ( 18) link_NAG-ASN : bond 0.00537 ( 15) link_NAG-ASN : angle 6.01395 ( 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 : 0.683 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: 0.1658 time to fit residues: 183.8768 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 : 0.709 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 255 GLN H 3 GLN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 567 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN C 188 GLN C 255 GLN ** 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 ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.107877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.077948 restraints weight = 54070.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081158 restraints weight = 30376.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.081558 restraints weight = 19254.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.082057 restraints weight = 16543.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082087 restraints weight = 15588.743| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19314 Z= 0.153 Angle : 0.724 9.903 26295 Z= 0.370 Chirality : 0.049 0.389 2952 Planarity : 0.005 0.042 3315 Dihedral : 9.586 75.273 3141 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: -0.87 (0.33), residues: 201 sheet: -1.14 (0.16), residues: 855 loop : -1.19 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 61 TYR 0.032 0.002 TYR M 96 PHE 0.033 0.002 PHE H 68 TRP 0.019 0.001 TRP A 104 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00330 (19266) covalent geometry : angle 0.69405 (26172) SS BOND : bond 0.00554 ( 21) SS BOND : angle 1.03540 ( 42) hydrogen bonds : bond 0.04704 ( 622) hydrogen bonds : angle 7.36440 ( 1749) link_ALPHA1-3 : bond 0.00934 ( 3) link_ALPHA1-3 : angle 1.94257 ( 9) link_ALPHA1-6 : bond 0.00300 ( 3) link_ALPHA1-6 : angle 2.02932 ( 9) link_BETA1-4 : bond 0.00322 ( 6) link_BETA1-4 : angle 3.37336 ( 18) link_NAG-ASN : bond 0.00660 ( 15) link_NAG-ASN : angle 4.36280 ( 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 708 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 708 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: 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: 0.8214 (t70) cc_final: 0.7906 (t70) REVERT: A 117 ASP cc_start: 0.8565 (p0) cc_final: 0.8231 (p0) REVERT: A 150 ASP cc_start: 0.8703 (m-30) cc_final: 0.8502 (m-30) REVERT: A 272 LYS cc_start: 0.5666 (pttt) cc_final: 0.5336 (ttmm) REVERT: H 12 VAL cc_start: 0.7023 (t) cc_final: 0.6491 (t) REVERT: H 45 LEU cc_start: 0.7555 (tp) cc_final: 0.7222 (tp) REVERT: H 86 LEU cc_start: 0.9153 (mt) cc_final: 0.8917 (mt) REVERT: K 46 LEU cc_start: 0.9036 (pt) cc_final: 0.8831 (pt) REVERT: K 81 GLU cc_start: 0.8690 (mp0) cc_final: 0.8374 (mp0) REVERT: K 82 ASP cc_start: 0.6864 (m-30) cc_final: 0.6219 (t0) REVERT: K 86 TYR cc_start: 0.6011 (m-10) cc_final: 0.3939 (m-10) REVERT: K 106 ILE cc_start: 0.2495 (mm) cc_final: 0.2196 (mm) REVERT: D 532 ILE cc_start: 0.9311 (mt) cc_final: 0.9095 (pt) REVERT: D 560 GLN cc_start: 0.9235 (tp40) cc_final: 0.8446 (tp40) REVERT: D 581 THR cc_start: 0.9608 (m) cc_final: 0.9354 (p) REVERT: D 592 PHE cc_start: 0.8452 (t80) cc_final: 0.8033 (t80) REVERT: Q 21 LEU cc_start: 0.8304 (tp) cc_final: 0.7973 (tp) REVERT: Q 61 ASP cc_start: 0.8061 (p0) cc_final: 0.7774 (p0) REVERT: N 15 SER cc_start: 0.8881 (m) cc_final: 0.8615 (p) REVERT: N 100 TRP cc_start: 0.9098 (t-100) cc_final: 0.8625 (t-100) REVERT: N 112 ASP cc_start: 0.9022 (p0) cc_final: 0.8573 (p0) REVERT: B 62 GLN cc_start: 0.9279 (mt0) cc_final: 0.8496 (mt0) REVERT: B 103 GLU cc_start: 0.8253 (tt0) cc_final: 0.7905 (tt0) REVERT: B 117 ASP cc_start: 0.8584 (p0) cc_final: 0.8167 (p0) REVERT: B 156 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7654 (mt-10) REVERT: I 34 MET cc_start: 0.7695 (mmm) cc_final: 0.7384 (mmp) REVERT: I 46 GLU cc_start: 0.8620 (pt0) cc_final: 0.8267 (pm20) REVERT: I 64 VAL cc_start: 0.9067 (m) cc_final: 0.8755 (m) REVERT: L 31 ASN cc_start: 0.7033 (p0) cc_final: 0.6405 (m-40) REVERT: L 36 TYR cc_start: 0.8317 (m-10) cc_final: 0.8061 (m-80) REVERT: L 73 LEU cc_start: 0.8319 (tp) cc_final: 0.8034 (tp) REVERT: L 89 GLN cc_start: 0.8291 (tt0) cc_final: 0.7991 (tt0) REVERT: L 90 GLN cc_start: 0.7735 (tp40) cc_final: 0.7004 (tp40) REVERT: E 532 ILE cc_start: 0.9309 (mt) cc_final: 0.9032 (pt) REVERT: E 534 TYR cc_start: 0.9289 (t80) cc_final: 0.9017 (t80) REVERT: E 573 LEU cc_start: 0.9606 (mt) cc_final: 0.9348 (mt) REVERT: E 581 THR cc_start: 0.9665 (m) cc_final: 0.9289 (p) REVERT: E 597 TRP cc_start: 0.7508 (t-100) cc_final: 0.7304 (t-100) REVERT: R 18 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7789 (ttp80) REVERT: R 21 LEU cc_start: 0.7971 (tt) cc_final: 0.7532 (mm) REVERT: R 36 TRP cc_start: 0.8504 (m100) cc_final: 0.8253 (m100) REVERT: R 61 ASP cc_start: 0.8294 (p0) cc_final: 0.8022 (t0) REVERT: O 58 ASN cc_start: 0.8747 (t0) cc_final: 0.8252 (t0) REVERT: O 100 TRP cc_start: 0.9118 (t-100) cc_final: 0.8624 (t-100) REVERT: C 57 LEU cc_start: 0.9196 (tp) cc_final: 0.8963 (mp) REVERT: C 62 GLN cc_start: 0.9306 (mt0) cc_final: 0.8654 (mt0) REVERT: C 68 LEU cc_start: 0.9434 (mt) cc_final: 0.9231 (mt) REVERT: C 117 ASP cc_start: 0.8534 (p0) cc_final: 0.8265 (p0) REVERT: C 273 LEU cc_start: 0.7647 (mp) cc_final: 0.7282 (mp) REVERT: J 12 VAL cc_start: 0.6758 (t) cc_final: 0.6445 (t) REVERT: J 36 TRP cc_start: 0.6875 (m100) cc_final: 0.5878 (m100) REVERT: J 46 GLU cc_start: 0.8765 (pt0) cc_final: 0.8317 (pm20) REVERT: J 57 LYS cc_start: 0.8848 (tppt) cc_final: 0.8438 (tttm) REVERT: J 83 MET cc_start: 0.8779 (mtt) cc_final: 0.8365 (mmm) REVERT: J 86 LEU cc_start: 0.9107 (mt) cc_final: 0.8904 (mt) REVERT: J 102 GLN cc_start: 0.8166 (mt0) cc_final: 0.7699 (mt0) REVERT: J 128 THR cc_start: 0.9139 (m) cc_final: 0.8812 (t) REVERT: M 31 ASN cc_start: 0.7195 (p0) cc_final: 0.6918 (m-40) REVERT: M 58 VAL cc_start: 0.7177 (t) cc_final: 0.6885 (p) REVERT: M 73 LEU cc_start: 0.8166 (tp) cc_final: 0.7683 (tp) REVERT: M 86 TYR cc_start: 0.6423 (m-10) cc_final: 0.5991 (m-80) REVERT: M 90 GLN cc_start: 0.7748 (tp40) cc_final: 0.7322 (tp40) REVERT: M 104 LEU cc_start: 0.7683 (tp) cc_final: 0.6528 (tp) REVERT: F 581 THR cc_start: 0.9654 (m) cc_final: 0.9366 (p) REVERT: S 4 LEU cc_start: 0.8698 (mt) cc_final: 0.8316 (mt) REVERT: S 43 GLN cc_start: 0.8504 (mp10) cc_final: 0.8297 (mp10) REVERT: S 61 ASP cc_start: 0.8193 (p0) cc_final: 0.7846 (t0) REVERT: S 62 ARG cc_start: 0.8451 (ptt-90) cc_final: 0.7684 (ptp90) REVERT: S 78 ARG cc_start: 0.8523 (ttp-170) cc_final: 0.7929 (ttp-170) REVERT: S 97 TYR cc_start: 0.8636 (m-80) cc_final: 0.8401 (m-80) REVERT: P 15 SER cc_start: 0.8955 (m) cc_final: 0.8495 (p) REVERT: P 32 TYR cc_start: 0.8794 (m-10) cc_final: 0.8237 (m-10) REVERT: P 60 ASN cc_start: 0.9212 (t0) cc_final: 0.8729 (t0) REVERT: P 100 TRP cc_start: 0.9076 (t-100) cc_final: 0.8628 (t-100) REVERT: P 111 MET cc_start: 0.8517 (mtm) cc_final: 0.8065 (mtt) REVERT: P 112 ASP cc_start: 0.8959 (p0) cc_final: 0.8503 (p0) outliers start: 0 outliers final: 0 residues processed: 708 average time/residue: 0.1377 time to fit residues: 147.7693 Evaluate side-chains 502 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN I 3 GLN I 74 ASN ** 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** ** E 567 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.105063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.074786 restraints weight = 54728.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.077145 restraints weight = 29893.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.078625 restraints weight = 20865.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079517 restraints weight = 16827.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.080039 restraints weight = 14852.095| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3460 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= 0.252 Angle : 0.762 11.816 26295 Z= 0.384 Chirality : 0.049 0.392 2952 Planarity : 0.005 0.045 3315 Dihedral : 8.988 67.371 3141 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % 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: -1.52 (0.17), residues: 2340 helix: 0.13 (0.36), residues: 183 sheet: -1.12 (0.16), residues: 942 loop : -0.99 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 18 TYR 0.028 0.002 TYR H 114 PHE 0.038 0.002 PHE Q 34 TRP 0.015 0.002 TRP O 114 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00571 (19266) covalent geometry : angle 0.73206 (26172) SS BOND : bond 0.00577 ( 21) SS BOND : angle 1.27927 ( 42) hydrogen bonds : bond 0.04235 ( 622) hydrogen bonds : angle 6.67850 ( 1749) link_ALPHA1-3 : bond 0.01196 ( 3) link_ALPHA1-3 : angle 1.80065 ( 9) link_ALPHA1-6 : bond 0.00040 ( 3) link_ALPHA1-6 : angle 2.11143 ( 9) link_BETA1-4 : bond 0.00562 ( 6) link_BETA1-4 : angle 3.12452 ( 18) link_NAG-ASN : bond 0.00536 ( 15) link_NAG-ASN : angle 4.53314 ( 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 604 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 603 time to evaluate : 0.714 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 39 HIS cc_start: 0.8237 (t70) cc_final: 0.7977 (t70) REVERT: A 62 GLN cc_start: 0.9175 (mt0) cc_final: 0.8795 (mt0) REVERT: A 78 ASP cc_start: 0.8353 (t70) cc_final: 0.8101 (t70) REVERT: A 117 ASP cc_start: 0.8424 (p0) cc_final: 0.8188 (p0) REVERT: H 102 GLN cc_start: 0.8414 (mt0) cc_final: 0.7727 (mt0) REVERT: H 114 TYR cc_start: 0.6503 (m-10) cc_final: 0.6137 (m-10) REVERT: K 46 LEU cc_start: 0.9112 (pt) cc_final: 0.8814 (pt) REVERT: K 81 GLU cc_start: 0.8621 (mp0) cc_final: 0.8267 (mp0) REVERT: K 89 GLN cc_start: 0.8346 (tt0) cc_final: 0.7997 (tt0) REVERT: D 512 ASN cc_start: 0.9340 (t0) cc_final: 0.9080 (t0) REVERT: D 581 THR cc_start: 0.9642 (m) cc_final: 0.9322 (p) REVERT: D 592 PHE cc_start: 0.8413 (t80) cc_final: 0.8049 (t80) REVERT: Q 34 PHE cc_start: 0.7871 (m-80) cc_final: 0.7629 (m-80) REVERT: Q 61 ASP cc_start: 0.8149 (p0) cc_final: 0.7900 (p0) REVERT: N 15 SER cc_start: 0.8793 (m) cc_final: 0.8513 (p) REVERT: N 112 ASP cc_start: 0.9001 (p0) cc_final: 0.8667 (p0) REVERT: B 62 GLN cc_start: 0.9314 (mt0) cc_final: 0.8517 (mt0) REVERT: B 117 ASP cc_start: 0.8499 (p0) cc_final: 0.8083 (p0) REVERT: B 272 LYS cc_start: 0.4603 (pttt) cc_final: 0.4018 (ttpp) REVERT: I 28 MET cc_start: 0.7159 (tmm) cc_final: 0.6692 (tmm) REVERT: I 46 GLU cc_start: 0.8695 (pt0) cc_final: 0.8324 (pm20) REVERT: I 48 MET cc_start: 0.8533 (mmm) cc_final: 0.8325 (tpp) REVERT: I 59 PHE cc_start: 0.7065 (t80) cc_final: 0.6584 (t80) REVERT: I 80 TYR cc_start: 0.8342 (m-80) cc_final: 0.8124 (m-80) REVERT: I 114 TYR cc_start: 0.6029 (m-10) cc_final: 0.5785 (m-80) REVERT: L 31 ASN cc_start: 0.7244 (p0) cc_final: 0.6643 (m-40) REVERT: L 73 LEU cc_start: 0.8435 (tp) cc_final: 0.8089 (tp) REVERT: L 93 SER cc_start: 0.8605 (p) cc_final: 0.8374 (t) REVERT: E 532 ILE cc_start: 0.9360 (mt) cc_final: 0.9128 (pt) REVERT: E 555 ILE cc_start: 0.9154 (mt) cc_final: 0.8857 (mt) REVERT: E 565 THR cc_start: 0.9213 (p) cc_final: 0.8779 (t) REVERT: E 581 THR cc_start: 0.9650 (m) cc_final: 0.9307 (p) REVERT: E 597 TRP cc_start: 0.7667 (t-100) cc_final: 0.7379 (t-100) REVERT: R 18 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7783 (ttp80) REVERT: R 61 ASP cc_start: 0.8322 (p0) cc_final: 0.8007 (t0) REVERT: O 112 ASP cc_start: 0.8882 (p0) cc_final: 0.8622 (p0) REVERT: C 62 GLN cc_start: 0.9330 (mt0) cc_final: 0.8482 (mt0) REVERT: C 68 LEU cc_start: 0.9511 (mt) cc_final: 0.9222 (mt) REVERT: C 117 ASP cc_start: 0.8367 (p0) cc_final: 0.8134 (p0) REVERT: J 12 VAL cc_start: 0.6864 (t) cc_final: 0.6565 (t) REVERT: J 46 GLU cc_start: 0.8692 (pt0) cc_final: 0.8274 (pm20) REVERT: J 80 TYR cc_start: 0.8168 (m-80) cc_final: 0.7956 (m-80) REVERT: J 82 GLN cc_start: 0.8110 (tp40) cc_final: 0.7858 (tp-100) REVERT: J 83 MET cc_start: 0.8683 (mtt) cc_final: 0.8416 (mmm) REVERT: J 101 LEU cc_start: 0.9086 (tp) cc_final: 0.8870 (tp) REVERT: J 102 GLN cc_start: 0.8225 (mt0) cc_final: 0.7886 (mt0) REVERT: J 128 THR cc_start: 0.9333 (m) cc_final: 0.9056 (t) REVERT: M 58 VAL cc_start: 0.7558 (t) cc_final: 0.7140 (p) REVERT: M 73 LEU cc_start: 0.8044 (tp) cc_final: 0.7660 (tp) REVERT: M 90 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7515 (tp40) REVERT: F 581 THR cc_start: 0.9662 (m) cc_final: 0.9319 (p) REVERT: S 4 LEU cc_start: 0.8497 (mt) cc_final: 0.8238 (mt) REVERT: S 61 ASP cc_start: 0.8215 (p0) cc_final: 0.7774 (t0) REVERT: P 15 SER cc_start: 0.8885 (m) cc_final: 0.8277 (p) REVERT: P 32 TYR cc_start: 0.8834 (m-10) cc_final: 0.8570 (m-10) REVERT: P 52 HIS cc_start: 0.7886 (t-90) cc_final: 0.7386 (t-90) REVERT: P 60 ASN cc_start: 0.9269 (t0) cc_final: 0.8856 (t0) REVERT: P 111 MET cc_start: 0.8641 (mtm) cc_final: 0.8186 (mtt) REVERT: P 112 ASP cc_start: 0.8869 (p0) cc_final: 0.8549 (p0) outliers start: 1 outliers final: 0 residues processed: 604 average time/residue: 0.1447 time to fit residues: 132.6315 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 : 0.661 ------------------------------------------------------------------------------- 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: 0.8980 chunk 135 optimal weight: 7.9990 chunk 130 optimal weight: 0.3980 chunk 192 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 D 508 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 GLN B 255 GLN I 31 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.107416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.078098 restraints weight = 54283.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080997 restraints weight = 29733.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081574 restraints weight = 19042.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082063 restraints weight = 16406.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082073 restraints weight = 15532.536| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19314 Z= 0.143 Angle : 0.688 9.942 26295 Z= 0.347 Chirality : 0.049 0.348 2952 Planarity : 0.004 0.071 3315 Dihedral : 8.079 57.098 3141 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.20 % Allowed : 2.36 % Favored : 97.44 % 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: -1.16 (0.17), residues: 2340 helix: 0.59 (0.37), residues: 183 sheet: -0.67 (0.17), residues: 891 loop : -0.99 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 52 TYR 0.033 0.002 TYR I 114 PHE 0.038 0.002 PHE Q 34 TRP 0.012 0.001 TRP N 114 HIS 0.006 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00322 (19266) covalent geometry : angle 0.66185 (26172) SS BOND : bond 0.00538 ( 21) SS BOND : angle 0.94547 ( 42) hydrogen bonds : bond 0.03622 ( 622) hydrogen bonds : angle 6.17808 ( 1749) link_ALPHA1-3 : bond 0.01094 ( 3) link_ALPHA1-3 : angle 1.58808 ( 9) link_ALPHA1-6 : bond 0.00328 ( 3) link_ALPHA1-6 : angle 1.91781 ( 9) link_BETA1-4 : bond 0.00451 ( 6) link_BETA1-4 : angle 3.04894 ( 18) link_NAG-ASN : bond 0.00556 ( 15) link_NAG-ASN : angle 4.03579 ( 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 601 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 597 time to evaluate : 0.713 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 39 HIS cc_start: 0.8286 (t70) cc_final: 0.8084 (t70) REVERT: A 56 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7311 (mmpt) REVERT: A 62 GLN cc_start: 0.9192 (mt0) cc_final: 0.8478 (mt0) REVERT: A 78 ASP cc_start: 0.8226 (t70) cc_final: 0.8010 (t70) REVERT: A 117 ASP cc_start: 0.8416 (p0) cc_final: 0.8066 (p0) REVERT: H 114 TYR cc_start: 0.6321 (m-10) cc_final: 0.5721 (m-10) REVERT: K 81 GLU cc_start: 0.8595 (mp0) cc_final: 0.8285 (mp0) REVERT: D 560 GLN cc_start: 0.8863 (tp40) cc_final: 0.8442 (tp40) REVERT: D 579 LEU cc_start: 0.8825 (mm) cc_final: 0.8451 (tp) REVERT: D 581 THR cc_start: 0.9588 (m) cc_final: 0.9253 (p) REVERT: D 591 ASP cc_start: 0.9045 (t0) cc_final: 0.8832 (t0) REVERT: Q 61 ASP cc_start: 0.8043 (p0) cc_final: 0.7816 (p0) REVERT: Q 79 LEU cc_start: 0.8386 (mt) cc_final: 0.8018 (mt) REVERT: N 15 SER cc_start: 0.8764 (m) cc_final: 0.8491 (p) REVERT: N 52 HIS cc_start: 0.7700 (t-90) cc_final: 0.6986 (t-90) REVERT: B 47 ASP cc_start: 0.6269 (t0) cc_final: 0.5875 (t0) REVERT: B 62 GLN cc_start: 0.9189 (mt0) cc_final: 0.8531 (mt0) REVERT: B 117 ASP cc_start: 0.8565 (p0) cc_final: 0.8139 (p0) REVERT: B 240 THR cc_start: 0.9498 (m) cc_final: 0.9274 (p) REVERT: I 46 GLU cc_start: 0.8614 (pt0) cc_final: 0.8207 (pm20) REVERT: I 48 MET cc_start: 0.8415 (mmm) cc_final: 0.7840 (tpp) REVERT: I 59 PHE cc_start: 0.7358 (t80) cc_final: 0.6921 (t80) REVERT: I 80 TYR cc_start: 0.8231 (m-80) cc_final: 0.7859 (m-80) REVERT: L 31 ASN cc_start: 0.7128 (p0) cc_final: 0.6675 (m-40) REVERT: L 73 LEU cc_start: 0.8357 (tp) cc_final: 0.7982 (tp) REVERT: L 104 LEU cc_start: 0.7752 (tp) cc_final: 0.7350 (tt) REVERT: E 532 ILE cc_start: 0.9205 (mt) cc_final: 0.8867 (pt) REVERT: E 534 TYR cc_start: 0.9293 (t80) cc_final: 0.8919 (t80) REVERT: E 555 ILE cc_start: 0.9065 (mt) cc_final: 0.8796 (mt) REVERT: E 564 GLU cc_start: 0.7829 (mp0) cc_final: 0.7610 (mp0) REVERT: E 565 THR cc_start: 0.9143 (p) cc_final: 0.8737 (t) REVERT: E 573 LEU cc_start: 0.9596 (mt) cc_final: 0.9390 (mt) REVERT: E 579 LEU cc_start: 0.8888 (mm) cc_final: 0.8481 (tp) REVERT: E 581 THR cc_start: 0.9618 (m) cc_final: 0.9283 (p) REVERT: R 18 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7662 (ttp80) REVERT: R 61 ASP cc_start: 0.8282 (p0) cc_final: 0.7928 (t0) REVERT: R 96 LEU cc_start: 0.9473 (mt) cc_final: 0.9091 (tt) REVERT: O 16 GLU cc_start: 0.8705 (pt0) cc_final: 0.8413 (pt0) REVERT: C 39 HIS cc_start: 0.8362 (t70) cc_final: 0.8064 (t70) REVERT: C 56 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7549 (mmmt) REVERT: C 62 GLN cc_start: 0.9093 (mt0) cc_final: 0.8406 (mt0) REVERT: C 68 LEU cc_start: 0.9408 (mt) cc_final: 0.9061 (mt) REVERT: J 12 VAL cc_start: 0.6812 (t) cc_final: 0.6528 (t) REVERT: J 28 MET cc_start: 0.8439 (tpt) cc_final: 0.8220 (tpt) REVERT: J 35 HIS cc_start: 0.8137 (m-70) cc_final: 0.7872 (m90) REVERT: J 36 TRP cc_start: 0.7149 (m100) cc_final: 0.6776 (m100) REVERT: J 43 LYS cc_start: 0.8382 (mppt) cc_final: 0.8177 (mppt) REVERT: J 46 GLU cc_start: 0.8788 (pt0) cc_final: 0.8331 (pm20) REVERT: J 82 GLN cc_start: 0.8024 (tp40) cc_final: 0.7787 (tp-100) REVERT: J 83 MET cc_start: 0.8703 (mtt) cc_final: 0.8370 (mmm) REVERT: J 102 GLN cc_start: 0.8226 (mt0) cc_final: 0.7310 (mt0) REVERT: J 114 TYR cc_start: 0.6268 (m-10) cc_final: 0.5660 (m-10) REVERT: J 128 THR cc_start: 0.9332 (m) cc_final: 0.9086 (t) REVERT: M 24 ARG cc_start: 0.7347 (mmm-85) cc_final: 0.6931 (mmm-85) REVERT: M 73 LEU cc_start: 0.8028 (tp) cc_final: 0.7550 (tp) REVERT: M 90 GLN cc_start: 0.7744 (tp-100) cc_final: 0.7261 (tp40) REVERT: F 581 THR cc_start: 0.9614 (m) cc_final: 0.9313 (p) REVERT: F 592 PHE cc_start: 0.8353 (t80) cc_final: 0.8044 (t80) REVERT: S 4 LEU cc_start: 0.8447 (mt) cc_final: 0.8172 (mt) REVERT: S 61 ASP cc_start: 0.8152 (p0) cc_final: 0.7676 (t0) REVERT: P 15 SER cc_start: 0.8966 (m) cc_final: 0.8447 (p) REVERT: P 32 TYR cc_start: 0.8772 (m-10) cc_final: 0.8507 (m-10) REVERT: P 52 HIS cc_start: 0.7761 (t-90) cc_final: 0.7348 (t-90) REVERT: P 60 ASN cc_start: 0.9271 (t0) cc_final: 0.8847 (t0) REVERT: P 111 MET cc_start: 0.8362 (mtm) cc_final: 0.8078 (mtt) outliers start: 4 outliers final: 0 residues processed: 601 average time/residue: 0.1437 time to fit residues: 131.0499 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 : 0.689 ------------------------------------------------------------------------------- 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: 9.9990 chunk 170 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 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: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS H 82 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN B 255 GLN I 31 ASN ** 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** C 139 HIS C 255 GLN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.103519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.073784 restraints weight = 54892.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076362 restraints weight = 31279.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.076739 restraints weight = 20496.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.077352 restraints weight = 18817.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.077441 restraints weight = 16775.483| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 19314 Z= 0.299 Angle : 0.797 11.643 26295 Z= 0.397 Chirality : 0.051 0.357 2952 Planarity : 0.004 0.036 3315 Dihedral : 7.995 48.537 3141 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % 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: -1.28 (0.17), residues: 2340 helix: 0.53 (0.38), residues: 180 sheet: -0.77 (0.17), residues: 873 loop : -1.06 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 38 TYR 0.043 0.002 TYR I 114 PHE 0.018 0.003 PHE D 592 TRP 0.019 0.002 TRP O 114 HIS 0.009 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00680 (19266) covalent geometry : angle 0.76760 (26172) SS BOND : bond 0.00793 ( 21) SS BOND : angle 1.81193 ( 42) hydrogen bonds : bond 0.04010 ( 622) hydrogen bonds : angle 6.26831 ( 1749) link_ALPHA1-3 : bond 0.01052 ( 3) link_ALPHA1-3 : angle 2.05244 ( 9) link_ALPHA1-6 : bond 0.00163 ( 3) link_ALPHA1-6 : angle 2.19049 ( 9) link_BETA1-4 : bond 0.00529 ( 6) link_BETA1-4 : angle 2.96616 ( 18) link_NAG-ASN : bond 0.00423 ( 15) link_NAG-ASN : angle 4.44600 ( 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 544 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 0.650 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: 0.7822 (mmtt) cc_final: 0.7585 (mmpt) REVERT: A 62 GLN cc_start: 0.9294 (mt0) cc_final: 0.8647 (mt0) REVERT: A 78 ASP cc_start: 0.8356 (t70) cc_final: 0.8121 (t70) REVERT: A 117 ASP cc_start: 0.8518 (p0) cc_final: 0.8215 (p0) REVERT: H 59 PHE cc_start: 0.7163 (t80) cc_final: 0.6943 (t80) REVERT: H 86 LEU cc_start: 0.9142 (mt) cc_final: 0.8863 (mt) REVERT: H 114 TYR cc_start: 0.6389 (m-10) cc_final: 0.5902 (m-10) REVERT: H 115 TYR cc_start: 0.8845 (m-10) cc_final: 0.8554 (m-10) REVERT: K 81 GLU cc_start: 0.8639 (mp0) cc_final: 0.8364 (mp0) REVERT: K 82 ASP cc_start: 0.6891 (m-30) cc_final: 0.6508 (m-30) REVERT: D 512 ASN cc_start: 0.9252 (t0) cc_final: 0.8944 (t0) REVERT: D 564 GLU cc_start: 0.7897 (mp0) cc_final: 0.7597 (mp0) REVERT: D 565 THR cc_start: 0.9255 (p) cc_final: 0.8961 (t) REVERT: D 581 THR cc_start: 0.9641 (m) cc_final: 0.9330 (p) REVERT: Q 34 PHE cc_start: 0.8200 (m-80) cc_final: 0.7964 (m-10) REVERT: Q 61 ASP cc_start: 0.8235 (p0) cc_final: 0.8026 (p0) REVERT: Q 79 LEU cc_start: 0.8056 (mt) cc_final: 0.7651 (mt) REVERT: N 15 SER cc_start: 0.8700 (m) cc_final: 0.8373 (p) REVERT: B 47 ASP cc_start: 0.6516 (t0) cc_final: 0.6207 (t0) REVERT: B 62 GLN cc_start: 0.9152 (mt0) cc_final: 0.8551 (mt0) REVERT: B 117 ASP cc_start: 0.8731 (p0) cc_final: 0.8472 (p0) REVERT: B 272 LYS cc_start: 0.4571 (pttt) cc_final: 0.3994 (ttmm) REVERT: I 46 GLU cc_start: 0.8711 (pt0) cc_final: 0.8234 (pm20) REVERT: I 48 MET cc_start: 0.8476 (mmm) cc_final: 0.8265 (tpp) REVERT: I 59 PHE cc_start: 0.7506 (t80) cc_final: 0.6856 (t80) REVERT: I 80 TYR cc_start: 0.8316 (m-80) cc_final: 0.7863 (m-80) REVERT: I 83 MET cc_start: 0.8620 (mmm) cc_final: 0.7999 (mmp) REVERT: I 104 TYR cc_start: 0.5823 (m-80) cc_final: 0.5432 (m-80) REVERT: I 120 VAL cc_start: 0.8023 (t) cc_final: 0.7822 (t) REVERT: L 31 ASN cc_start: 0.7290 (p0) cc_final: 0.6715 (m-40) REVERT: L 61 ARG cc_start: 0.6440 (ptt-90) cc_final: 0.6203 (ptt-90) REVERT: L 73 LEU cc_start: 0.8391 (tp) cc_final: 0.8052 (tp) REVERT: E 532 ILE cc_start: 0.9251 (mt) cc_final: 0.8982 (pt) REVERT: E 555 ILE cc_start: 0.9311 (mt) cc_final: 0.9018 (mt) REVERT: E 565 THR cc_start: 0.9280 (p) cc_final: 0.8902 (t) REVERT: E 573 LEU cc_start: 0.9671 (mt) cc_final: 0.9453 (mt) REVERT: E 581 THR cc_start: 0.9639 (m) cc_final: 0.9300 (p) REVERT: E 597 TRP cc_start: 0.7672 (t-100) cc_final: 0.7184 (t-100) REVERT: R 61 ASP cc_start: 0.8410 (p0) cc_final: 0.7957 (t0) REVERT: R 96 LEU cc_start: 0.9465 (mt) cc_final: 0.9245 (mt) REVERT: O 16 GLU cc_start: 0.8680 (pt0) cc_final: 0.8287 (pt0) REVERT: O 112 ASP cc_start: 0.8994 (p0) cc_final: 0.8346 (p0) REVERT: C 62 GLN cc_start: 0.9117 (mt0) cc_final: 0.8529 (mt0) REVERT: C 117 ASP cc_start: 0.8667 (p0) cc_final: 0.8452 (p0) REVERT: C 172 ARG cc_start: 0.8765 (ttm110) cc_final: 0.8084 (ttm110) REVERT: J 12 VAL cc_start: 0.6704 (t) cc_final: 0.6404 (t) REVERT: J 31 ASN cc_start: 0.8377 (t0) cc_final: 0.8148 (t0) REVERT: J 35 HIS cc_start: 0.8244 (m-70) cc_final: 0.7890 (m170) REVERT: J 36 TRP cc_start: 0.7283 (m100) cc_final: 0.6958 (m100) REVERT: J 43 LYS cc_start: 0.8503 (mppt) cc_final: 0.8102 (mppt) REVERT: J 46 GLU cc_start: 0.8832 (pt0) cc_final: 0.8315 (pm20) REVERT: J 82 GLN cc_start: 0.8087 (tp40) cc_final: 0.7795 (tp-100) REVERT: J 83 MET cc_start: 0.8832 (mtt) cc_final: 0.8438 (mmm) REVERT: J 86 LEU cc_start: 0.9183 (mt) cc_final: 0.8860 (mt) REVERT: J 102 GLN cc_start: 0.8356 (mt0) cc_final: 0.7404 (mt0) REVERT: J 114 TYR cc_start: 0.6194 (m-10) cc_final: 0.5704 (m-10) REVERT: J 128 THR cc_start: 0.9379 (m) cc_final: 0.9155 (t) REVERT: M 24 ARG cc_start: 0.7439 (mmm-85) cc_final: 0.7052 (mmm-85) REVERT: M 55 GLN cc_start: 0.7464 (tm-30) cc_final: 0.7169 (tm-30) REVERT: M 73 LEU cc_start: 0.8017 (tp) cc_final: 0.7551 (tp) REVERT: M 90 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7521 (tp40) REVERT: F 581 THR cc_start: 0.9658 (m) cc_final: 0.9327 (p) REVERT: F 592 PHE cc_start: 0.8260 (t80) cc_final: 0.7858 (t80) REVERT: S 4 LEU cc_start: 0.8474 (mt) cc_final: 0.8152 (mt) REVERT: P 15 SER cc_start: 0.8898 (m) cc_final: 0.8352 (p) REVERT: P 32 TYR cc_start: 0.8866 (m-10) cc_final: 0.8568 (m-10) REVERT: P 60 ASN cc_start: 0.9304 (t0) cc_final: 0.8926 (t0) REVERT: P 111 MET cc_start: 0.8596 (mtm) cc_final: 0.8222 (mtp) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.1360 time to fit residues: 112.9455 Evaluate side-chains 443 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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: 0.6980 chunk 56 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN B 255 GLN I 31 ASN ** 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** ** 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN F 567 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074482 restraints weight = 54788.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.077375 restraints weight = 30471.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077778 restraints weight = 19670.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.078208 restraints weight = 17287.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.078338 restraints weight = 16212.605| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 19314 Z= 0.243 Angle : 0.746 11.291 26295 Z= 0.373 Chirality : 0.050 0.365 2952 Planarity : 0.004 0.041 3315 Dihedral : 7.444 39.325 3141 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % 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: 0.48 (0.38), residues: 183 sheet: -0.77 (0.17), residues: 888 loop : -1.06 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 61 TYR 0.047 0.002 TYR I 114 PHE 0.018 0.002 PHE I 29 TRP 0.015 0.002 TRP O 114 HIS 0.006 0.001 HIS I 112 Details of bonding type rmsd covalent geometry : bond 0.00553 (19266) covalent geometry : angle 0.71751 (26172) SS BOND : bond 0.00587 ( 21) SS BOND : angle 1.79772 ( 42) hydrogen bonds : bond 0.03722 ( 622) hydrogen bonds : angle 6.07717 ( 1749) link_ALPHA1-3 : bond 0.01095 ( 3) link_ALPHA1-3 : angle 1.91608 ( 9) link_ALPHA1-6 : bond 0.00230 ( 3) link_ALPHA1-6 : angle 2.12311 ( 9) link_BETA1-4 : bond 0.00523 ( 6) link_BETA1-4 : angle 2.91133 ( 18) link_NAG-ASN : bond 0.00466 ( 15) link_NAG-ASN : angle 4.25041 ( 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 544 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 0.727 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: A 56 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7560 (mmpt) REVERT: A 62 GLN cc_start: 0.9251 (mt0) cc_final: 0.8595 (mt0) REVERT: A 103 GLU cc_start: 0.8418 (tt0) cc_final: 0.8185 (tt0) REVERT: A 117 ASP cc_start: 0.8615 (p0) cc_final: 0.8340 (p0) REVERT: H 52 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.8517 (mtm-85) REVERT: H 59 PHE cc_start: 0.7154 (t80) cc_final: 0.6810 (t80) REVERT: H 86 LEU cc_start: 0.9101 (mt) cc_final: 0.8848 (mt) REVERT: H 114 TYR cc_start: 0.6349 (m-10) cc_final: 0.5807 (m-10) REVERT: H 115 TYR cc_start: 0.8862 (m-10) cc_final: 0.8599 (m-10) REVERT: K 81 GLU cc_start: 0.8698 (mp0) cc_final: 0.8411 (mp0) REVERT: D 512 ASN cc_start: 0.9199 (t0) cc_final: 0.8869 (t0) REVERT: D 565 THR cc_start: 0.9269 (p) cc_final: 0.8972 (t) REVERT: D 592 PHE cc_start: 0.8415 (t80) cc_final: 0.8133 (t80) REVERT: Q 61 ASP cc_start: 0.8184 (p0) cc_final: 0.7886 (p0) REVERT: N 15 SER cc_start: 0.8720 (m) cc_final: 0.8363 (p) REVERT: B 47 ASP cc_start: 0.6517 (t0) cc_final: 0.6031 (t0) REVERT: B 62 GLN cc_start: 0.9166 (mt0) cc_final: 0.8597 (mt0) REVERT: B 117 ASP cc_start: 0.8640 (p0) cc_final: 0.8407 (p0) REVERT: I 46 GLU cc_start: 0.8756 (pt0) cc_final: 0.8275 (pm20) REVERT: I 48 MET cc_start: 0.8395 (mmm) cc_final: 0.7857 (tpp) REVERT: I 59 PHE cc_start: 0.7436 (t80) cc_final: 0.6697 (t80) REVERT: I 80 TYR cc_start: 0.8279 (m-80) cc_final: 0.7887 (m-80) REVERT: I 83 MET cc_start: 0.8631 (mmm) cc_final: 0.7975 (mmp) REVERT: L 31 ASN cc_start: 0.7315 (p0) cc_final: 0.6647 (m-40) REVERT: L 73 LEU cc_start: 0.8405 (tp) cc_final: 0.8032 (tp) REVERT: E 532 ILE cc_start: 0.9253 (mt) cc_final: 0.8981 (pt) REVERT: E 555 ILE cc_start: 0.9284 (mt) cc_final: 0.8973 (mt) REVERT: E 565 THR cc_start: 0.9236 (p) cc_final: 0.8963 (t) REVERT: E 581 THR cc_start: 0.9620 (m) cc_final: 0.9293 (p) REVERT: E 597 TRP cc_start: 0.7584 (t-100) cc_final: 0.7378 (t-100) REVERT: R 61 ASP cc_start: 0.8417 (p0) cc_final: 0.7967 (t0) REVERT: R 96 LEU cc_start: 0.9471 (mt) cc_final: 0.9084 (tt) REVERT: O 16 GLU cc_start: 0.8637 (pt0) cc_final: 0.8241 (pt0) REVERT: O 112 ASP cc_start: 0.8841 (p0) cc_final: 0.8461 (p0) REVERT: C 62 GLN cc_start: 0.9070 (mt0) cc_final: 0.8483 (mt0) REVERT: C 172 ARG cc_start: 0.8718 (ttm110) cc_final: 0.8075 (ttm110) REVERT: J 12 VAL cc_start: 0.6701 (t) cc_final: 0.6378 (t) REVERT: J 43 LYS cc_start: 0.8495 (mppt) cc_final: 0.8097 (mppt) REVERT: J 46 GLU cc_start: 0.8842 (pt0) cc_final: 0.8401 (pm20) REVERT: J 59 PHE cc_start: 0.7233 (t80) cc_final: 0.6980 (t80) REVERT: J 64 VAL cc_start: 0.9052 (m) cc_final: 0.8634 (t) REVERT: J 83 MET cc_start: 0.8837 (mtt) cc_final: 0.8555 (mmm) REVERT: J 101 LEU cc_start: 0.9109 (tp) cc_final: 0.8748 (tp) REVERT: J 102 GLN cc_start: 0.8277 (mt0) cc_final: 0.7818 (mt0) REVERT: J 128 THR cc_start: 0.9346 (m) cc_final: 0.9145 (t) REVERT: M 24 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.7244 (mmm-85) REVERT: M 55 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7307 (tm-30) REVERT: M 69 THR cc_start: 0.8510 (p) cc_final: 0.8308 (p) REVERT: M 73 LEU cc_start: 0.7990 (tp) cc_final: 0.7491 (tp) REVERT: M 75 ILE cc_start: 0.7109 (mt) cc_final: 0.6791 (mt) REVERT: F 592 PHE cc_start: 0.8280 (t80) cc_final: 0.7866 (t80) REVERT: S 4 LEU cc_start: 0.8429 (mt) cc_final: 0.8146 (mt) REVERT: P 15 SER cc_start: 0.8917 (m) cc_final: 0.8378 (p) REVERT: P 32 TYR cc_start: 0.8804 (m-10) cc_final: 0.8557 (m-10) REVERT: P 60 ASN cc_start: 0.9312 (t0) cc_final: 0.8966 (t0) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.1405 time to fit residues: 114.9218 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 : 0.654 ------------------------------------------------------------------------------- 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: 0.8980 chunk 146 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 255 GLN ** H 31 ASN ** 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 I 74 ASN ** 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** E 521 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN F 521 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN P 39 GLN P 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.071717 restraints weight = 55672.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.073903 restraints weight = 31361.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.075305 restraints weight = 22184.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076171 restraints weight = 18066.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076663 restraints weight = 16000.842| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 19314 Z= 0.342 Angle : 0.849 12.696 26295 Z= 0.421 Chirality : 0.052 0.375 2952 Planarity : 0.005 0.040 3315 Dihedral : 7.451 40.175 3141 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 0.22 (0.37), residues: 183 sheet: -1.08 (0.16), residues: 951 loop : -1.07 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 38 TYR 0.024 0.003 TYR O 50 PHE 0.054 0.003 PHE Q 34 TRP 0.025 0.003 TRP H 108 HIS 0.012 0.002 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00771 (19266) covalent geometry : angle 0.81995 (26172) SS BOND : bond 0.00732 ( 21) SS BOND : angle 2.23059 ( 42) hydrogen bonds : bond 0.04023 ( 622) hydrogen bonds : angle 6.28141 ( 1749) link_ALPHA1-3 : bond 0.00996 ( 3) link_ALPHA1-3 : angle 2.40850 ( 9) link_ALPHA1-6 : bond 0.00114 ( 3) link_ALPHA1-6 : angle 2.23132 ( 9) link_BETA1-4 : bond 0.00593 ( 6) link_BETA1-4 : angle 2.89728 ( 18) link_NAG-ASN : bond 0.00416 ( 15) link_NAG-ASN : angle 4.48262 ( 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 518 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 0.712 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: A 56 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7474 (mmmt) REVERT: A 62 GLN cc_start: 0.9177 (mt0) cc_final: 0.8577 (mt0) REVERT: A 103 GLU cc_start: 0.8412 (tt0) cc_final: 0.8211 (tt0) REVERT: A 117 ASP cc_start: 0.8490 (p0) cc_final: 0.8185 (p0) REVERT: H 52 ARG cc_start: 0.8945 (mtm-85) cc_final: 0.8461 (mtm-85) REVERT: H 59 PHE cc_start: 0.7252 (t80) cc_final: 0.6760 (t80) REVERT: H 86 LEU cc_start: 0.9053 (mt) cc_final: 0.8698 (mt) REVERT: H 114 TYR cc_start: 0.6418 (m-10) cc_final: 0.5928 (m-10) REVERT: K 81 GLU cc_start: 0.8680 (mp0) cc_final: 0.8460 (mp0) REVERT: D 512 ASN cc_start: 0.9151 (t0) cc_final: 0.8801 (t0) REVERT: D 592 PHE cc_start: 0.8343 (t80) cc_final: 0.8123 (t80) REVERT: Q 61 ASP cc_start: 0.8348 (p0) cc_final: 0.8028 (p0) REVERT: Q 78 ARG cc_start: 0.8271 (tmm-80) cc_final: 0.8017 (ttp-170) REVERT: N 15 SER cc_start: 0.8666 (m) cc_final: 0.8247 (p) REVERT: B 47 ASP cc_start: 0.6447 (t0) cc_final: 0.5900 (t0) REVERT: B 62 GLN cc_start: 0.9090 (mt0) cc_final: 0.8557 (mt0) REVERT: B 103 GLU cc_start: 0.8383 (tt0) cc_final: 0.8167 (tt0) REVERT: B 272 LYS cc_start: 0.5164 (pttt) cc_final: 0.4677 (ttmm) REVERT: I 46 GLU cc_start: 0.8705 (pt0) cc_final: 0.8250 (pm20) REVERT: I 80 TYR cc_start: 0.8261 (m-80) cc_final: 0.7907 (m-80) REVERT: I 83 MET cc_start: 0.8639 (mmm) cc_final: 0.7954 (mmp) REVERT: L 31 ASN cc_start: 0.7212 (p0) cc_final: 0.6591 (m-40) REVERT: L 55 GLN cc_start: 0.7344 (tm-30) cc_final: 0.7113 (tm-30) REVERT: L 73 LEU cc_start: 0.8264 (tp) cc_final: 0.7881 (tp) REVERT: E 532 ILE cc_start: 0.9272 (mt) cc_final: 0.9026 (pt) REVERT: E 555 ILE cc_start: 0.9382 (mt) cc_final: 0.9115 (mt) REVERT: E 564 GLU cc_start: 0.7922 (mp0) cc_final: 0.7722 (mp0) REVERT: E 565 THR cc_start: 0.9229 (p) cc_final: 0.8868 (t) REVERT: E 581 THR cc_start: 0.9584 (m) cc_final: 0.9227 (p) REVERT: E 592 PHE cc_start: 0.8349 (t80) cc_final: 0.7911 (t80) REVERT: R 61 ASP cc_start: 0.8396 (p0) cc_final: 0.7886 (t0) REVERT: R 76 ILE cc_start: 0.9359 (mp) cc_final: 0.9035 (tt) REVERT: R 96 LEU cc_start: 0.9440 (mt) cc_final: 0.9232 (mt) REVERT: O 16 GLU cc_start: 0.8592 (pt0) cc_final: 0.8230 (pt0) REVERT: O 112 ASP cc_start: 0.8742 (p0) cc_final: 0.8429 (p0) REVERT: C 56 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7380 (mmmt) REVERT: C 62 GLN cc_start: 0.9126 (mt0) cc_final: 0.8558 (mt0) REVERT: J 12 VAL cc_start: 0.6790 (t) cc_final: 0.6476 (t) REVERT: J 31 ASN cc_start: 0.8200 (t0) cc_final: 0.8000 (t0) REVERT: J 46 GLU cc_start: 0.8918 (pt0) cc_final: 0.8420 (pm20) REVERT: J 59 PHE cc_start: 0.7186 (t80) cc_final: 0.6890 (t80) REVERT: J 87 ARG cc_start: 0.8204 (mmp80) cc_final: 0.7998 (mmp80) REVERT: J 101 LEU cc_start: 0.9118 (tp) cc_final: 0.8823 (tp) REVERT: J 102 GLN cc_start: 0.8264 (mt0) cc_final: 0.7536 (mt0) REVERT: J 114 TYR cc_start: 0.6376 (m-10) cc_final: 0.5644 (m-10) REVERT: M 55 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7413 (tm-30) REVERT: M 73 LEU cc_start: 0.8088 (tp) cc_final: 0.7611 (tp) REVERT: F 592 PHE cc_start: 0.8293 (t80) cc_final: 0.7856 (t80) REVERT: P 15 SER cc_start: 0.8821 (m) cc_final: 0.7961 (p) REVERT: P 32 TYR cc_start: 0.8867 (m-10) cc_final: 0.8568 (m-10) REVERT: P 60 ASN cc_start: 0.9320 (t0) cc_final: 0.9033 (t0) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.1357 time to fit residues: 107.8580 Evaluate side-chains 416 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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: 0.9990 chunk 154 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 144 optimal weight: 0.4980 chunk 169 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** 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 39 GLN N 76 ASN B 255 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 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 6 GLN ** 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 = 0.3618 r_free = 0.3618 target = 0.106346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076298 restraints weight = 54204.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078666 restraints weight = 29888.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080212 restraints weight = 20865.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.081084 restraints weight = 16777.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081649 restraints weight = 14852.243| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19314 Z= 0.138 Angle : 0.730 10.642 26295 Z= 0.364 Chirality : 0.050 0.336 2952 Planarity : 0.004 0.041 3315 Dihedral : 6.803 38.423 3141 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -1.09 (0.17), residues: 2340 helix: 0.49 (0.37), residues: 183 sheet: -0.60 (0.17), residues: 870 loop : -0.94 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 18 TYR 0.019 0.002 TYR J 116 PHE 0.016 0.002 PHE J 50 TRP 0.018 0.001 TRP B 275 HIS 0.011 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00309 (19266) covalent geometry : angle 0.70484 (26172) SS BOND : bond 0.00638 ( 21) SS BOND : angle 1.47414 ( 42) hydrogen bonds : bond 0.03515 ( 622) hydrogen bonds : angle 5.82989 ( 1749) link_ALPHA1-3 : bond 0.01309 ( 3) link_ALPHA1-3 : angle 1.64627 ( 9) link_ALPHA1-6 : bond 0.00521 ( 3) link_ALPHA1-6 : angle 1.70359 ( 9) link_BETA1-4 : bond 0.00561 ( 6) link_BETA1-4 : angle 2.77884 ( 18) link_NAG-ASN : bond 0.00605 ( 15) link_NAG-ASN : angle 3.97874 ( 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 562 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.489 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: A 78 ASP cc_start: 0.8089 (t70) cc_final: 0.7809 (t70) REVERT: H 52 ARG cc_start: 0.8999 (mtm-85) cc_final: 0.8492 (mtm-85) REVERT: H 59 PHE cc_start: 0.7079 (t80) cc_final: 0.6708 (t80) REVERT: H 60 TYR cc_start: 0.7863 (m-80) cc_final: 0.7634 (m-80) REVERT: H 114 TYR cc_start: 0.6196 (m-10) cc_final: 0.5669 (m-10) REVERT: H 115 TYR cc_start: 0.8797 (m-10) cc_final: 0.8577 (m-10) REVERT: K 81 GLU cc_start: 0.8693 (mp0) cc_final: 0.8469 (mp0) REVERT: D 512 ASN cc_start: 0.9160 (t0) cc_final: 0.8744 (t0) REVERT: D 560 GLN cc_start: 0.9129 (tp40) cc_final: 0.8224 (tp40) REVERT: D 565 THR cc_start: 0.9237 (p) cc_final: 0.8950 (t) REVERT: D 578 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8053 (mm-30) REVERT: D 579 LEU cc_start: 0.9084 (mm) cc_final: 0.8864 (tp) REVERT: D 592 PHE cc_start: 0.8247 (t80) cc_final: 0.7948 (t80) REVERT: Q 33 TYR cc_start: 0.7788 (m-10) cc_final: 0.7525 (m-10) REVERT: N 15 SER cc_start: 0.8646 (m) cc_final: 0.8231 (p) REVERT: N 52 HIS cc_start: 0.8028 (t-90) cc_final: 0.7616 (t70) REVERT: B 47 ASP cc_start: 0.6625 (t0) cc_final: 0.6069 (t0) REVERT: B 62 GLN cc_start: 0.9067 (mt0) cc_final: 0.8554 (mt0) REVERT: B 117 ASP cc_start: 0.8697 (p0) cc_final: 0.8426 (p0) REVERT: I 31 ASN cc_start: 0.8650 (p0) cc_final: 0.7728 (m110) REVERT: I 46 GLU cc_start: 0.8647 (pt0) cc_final: 0.8152 (pm20) REVERT: I 59 PHE cc_start: 0.7038 (t80) cc_final: 0.6585 (t80) REVERT: I 80 TYR cc_start: 0.8211 (m-80) cc_final: 0.7934 (m-80) REVERT: I 83 MET cc_start: 0.8719 (mmm) cc_final: 0.8063 (mmp) REVERT: L 31 ASN cc_start: 0.7115 (p0) cc_final: 0.6406 (m-40) REVERT: L 55 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7101 (tm-30) REVERT: L 70 ASP cc_start: 0.7256 (t0) cc_final: 0.6813 (p0) REVERT: L 73 LEU cc_start: 0.8393 (tp) cc_final: 0.7972 (tp) REVERT: E 514 ASN cc_start: 0.9193 (m-40) cc_final: 0.8754 (m-40) REVERT: E 555 ILE cc_start: 0.9224 (mt) cc_final: 0.8921 (mt) REVERT: E 560 GLN cc_start: 0.8915 (tp40) cc_final: 0.7757 (tp40) REVERT: E 564 GLU cc_start: 0.7840 (mp0) cc_final: 0.7459 (mp0) REVERT: E 565 THR cc_start: 0.9186 (p) cc_final: 0.8858 (t) REVERT: E 579 LEU cc_start: 0.9128 (mm) cc_final: 0.8807 (tp) REVERT: E 581 THR cc_start: 0.9558 (m) cc_final: 0.9205 (p) REVERT: R 18 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7721 (ttp80) REVERT: R 61 ASP cc_start: 0.8296 (p0) cc_final: 0.7854 (t0) REVERT: R 82 GLU cc_start: 0.8218 (pm20) cc_final: 0.7701 (pm20) REVERT: R 96 LEU cc_start: 0.9389 (mt) cc_final: 0.9034 (tt) REVERT: O 16 GLU cc_start: 0.8466 (pt0) cc_final: 0.8181 (pt0) REVERT: C 56 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7352 (mmmt) REVERT: C 62 GLN cc_start: 0.9013 (mt0) cc_final: 0.8479 (mt0) REVERT: C 68 LEU cc_start: 0.9382 (mt) cc_final: 0.9010 (mt) REVERT: J 12 VAL cc_start: 0.6826 (t) cc_final: 0.6481 (t) REVERT: J 46 GLU cc_start: 0.8822 (pt0) cc_final: 0.8396 (pm20) REVERT: J 48 MET cc_start: 0.8439 (mmm) cc_final: 0.8100 (tpp) REVERT: J 59 PHE cc_start: 0.7213 (t80) cc_final: 0.6716 (t80) REVERT: J 86 LEU cc_start: 0.9023 (mt) cc_final: 0.8702 (mt) REVERT: J 101 LEU cc_start: 0.8982 (tp) cc_final: 0.8002 (mt) REVERT: J 102 GLN cc_start: 0.8159 (mt0) cc_final: 0.7219 (mt0) REVERT: J 114 TYR cc_start: 0.6317 (m-10) cc_final: 0.5529 (m-10) REVERT: J 128 THR cc_start: 0.9310 (p) cc_final: 0.9085 (t) REVERT: M 24 ARG cc_start: 0.7020 (mmm-85) cc_final: 0.6652 (mmm-85) REVERT: M 55 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7356 (tm-30) REVERT: M 73 LEU cc_start: 0.7974 (tp) cc_final: 0.7419 (tp) REVERT: F 560 GLN cc_start: 0.9164 (tp40) cc_final: 0.7976 (tp40) REVERT: F 592 PHE cc_start: 0.8270 (t80) cc_final: 0.7957 (t80) REVERT: S 78 ARG cc_start: 0.8506 (ttp-170) cc_final: 0.7944 (ttp-170) REVERT: P 15 SER cc_start: 0.8745 (m) cc_final: 0.7818 (p) REVERT: P 32 TYR cc_start: 0.8756 (m-10) cc_final: 0.8548 (m-10) REVERT: P 60 ASN cc_start: 0.9268 (t0) cc_final: 0.8929 (t0) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 0.1301 time to fit residues: 111.8855 Evaluate side-chains 468 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 0.6980 chunk 3 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 63 optimal weight: 0.0670 chunk 108 optimal weight: 0.9980 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 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** ** 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** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076929 restraints weight = 54346.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.079328 restraints weight = 29951.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.080845 restraints weight = 20826.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.081770 restraints weight = 16790.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.082303 restraints weight = 14791.167| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19314 Z= 0.139 Angle : 0.723 11.792 26295 Z= 0.361 Chirality : 0.049 0.317 2952 Planarity : 0.004 0.064 3315 Dihedral : 6.428 37.866 3141 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -0.88 (0.17), residues: 2340 helix: 0.76 (0.38), residues: 183 sheet: -0.34 (0.18), residues: 837 loop : -0.91 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 172 TYR 0.020 0.002 TYR F 534 PHE 0.020 0.001 PHE Q 99 TRP 0.037 0.002 TRP L 35 HIS 0.012 0.001 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00315 (19266) covalent geometry : angle 0.70007 (26172) SS BOND : bond 0.00493 ( 21) SS BOND : angle 1.53441 ( 42) hydrogen bonds : bond 0.03475 ( 622) hydrogen bonds : angle 5.70099 ( 1749) link_ALPHA1-3 : bond 0.00940 ( 3) link_ALPHA1-3 : angle 1.30292 ( 9) link_ALPHA1-6 : bond 0.00478 ( 3) link_ALPHA1-6 : angle 1.57707 ( 9) link_BETA1-4 : bond 0.00454 ( 6) link_BETA1-4 : angle 2.97417 ( 18) link_NAG-ASN : bond 0.00548 ( 15) link_NAG-ASN : angle 3.76686 ( 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 565 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 565 time to evaluate : 0.616 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: 0.9036 (mt0) cc_final: 0.8433 (mt0) REVERT: A 78 ASP cc_start: 0.8088 (t70) cc_final: 0.7795 (t70) REVERT: A 253 LEU cc_start: 0.9368 (mp) cc_final: 0.9163 (mp) REVERT: A 272 LYS cc_start: 0.4667 (pttt) cc_final: 0.4373 (pttm) REVERT: H 52 ARG cc_start: 0.8998 (mtm-85) cc_final: 0.8480 (mtm-85) REVERT: H 59 PHE cc_start: 0.7039 (t80) cc_final: 0.6784 (t80) REVERT: H 60 TYR cc_start: 0.7834 (m-80) cc_final: 0.7557 (m-80) REVERT: H 114 TYR cc_start: 0.6204 (m-10) cc_final: 0.5730 (m-10) REVERT: K 69 THR cc_start: 0.8270 (p) cc_final: 0.7594 (p) REVERT: K 70 ASP cc_start: 0.7093 (p0) cc_final: 0.6650 (p0) REVERT: K 81 GLU cc_start: 0.8731 (mp0) cc_final: 0.8480 (mp0) REVERT: D 512 ASN cc_start: 0.9054 (t0) cc_final: 0.8819 (t0) REVERT: D 560 GLN cc_start: 0.8909 (tp40) cc_final: 0.8037 (tm-30) REVERT: D 565 THR cc_start: 0.9227 (p) cc_final: 0.8942 (t) REVERT: D 578 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8210 (mm-30) REVERT: D 579 LEU cc_start: 0.9098 (mm) cc_final: 0.8883 (tp) REVERT: Q 34 PHE cc_start: 0.7802 (m-80) cc_final: 0.7457 (m-80) REVERT: N 15 SER cc_start: 0.8570 (m) cc_final: 0.7445 (p) REVERT: B 47 ASP cc_start: 0.6682 (t0) cc_final: 0.6093 (t0) REVERT: B 62 GLN cc_start: 0.9105 (mt0) cc_final: 0.8668 (mt0) REVERT: B 117 ASP cc_start: 0.8707 (p0) cc_final: 0.8441 (p0) REVERT: I 31 ASN cc_start: 0.8616 (p0) cc_final: 0.7718 (m110) REVERT: I 46 GLU cc_start: 0.8679 (pt0) cc_final: 0.8279 (pm20) REVERT: I 59 PHE cc_start: 0.7088 (t80) cc_final: 0.6569 (t80) REVERT: I 83 MET cc_start: 0.8673 (mmm) cc_final: 0.7819 (mmp) REVERT: I 118 LEU cc_start: 0.8134 (tt) cc_final: 0.7706 (mm) REVERT: L 31 ASN cc_start: 0.7088 (p0) cc_final: 0.6702 (m-40) REVERT: L 55 GLN cc_start: 0.7538 (tm-30) cc_final: 0.7175 (tm-30) REVERT: L 70 ASP cc_start: 0.7341 (t0) cc_final: 0.6908 (p0) REVERT: E 514 ASN cc_start: 0.9071 (m-40) cc_final: 0.8406 (m-40) REVERT: E 555 ILE cc_start: 0.9168 (mt) cc_final: 0.8833 (mt) REVERT: E 560 GLN cc_start: 0.8894 (tp40) cc_final: 0.7648 (tp40) REVERT: E 564 GLU cc_start: 0.7841 (mp0) cc_final: 0.7532 (mp0) REVERT: E 565 THR cc_start: 0.9200 (p) cc_final: 0.8880 (t) REVERT: E 579 LEU cc_start: 0.9098 (mm) cc_final: 0.8833 (tp) REVERT: E 581 THR cc_start: 0.9552 (m) cc_final: 0.9188 (p) REVERT: R 18 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7570 (ttp80) REVERT: R 61 ASP cc_start: 0.8282 (p0) cc_final: 0.7804 (t0) REVERT: R 96 LEU cc_start: 0.9346 (mt) cc_final: 0.8984 (tt) REVERT: O 16 GLU cc_start: 0.8442 (pt0) cc_final: 0.8130 (pt0) REVERT: C 56 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7472 (mmmt) REVERT: C 62 GLN cc_start: 0.9068 (mt0) cc_final: 0.8614 (mt0) REVERT: C 68 LEU cc_start: 0.9345 (mt) cc_final: 0.9073 (mt) REVERT: J 12 VAL cc_start: 0.6853 (t) cc_final: 0.6525 (t) REVERT: J 46 GLU cc_start: 0.8786 (pt0) cc_final: 0.8420 (pm20) REVERT: J 59 PHE cc_start: 0.7267 (t80) cc_final: 0.6781 (t80) REVERT: J 80 TYR cc_start: 0.8188 (m-80) cc_final: 0.7981 (m-80) REVERT: J 86 LEU cc_start: 0.8929 (mt) cc_final: 0.8688 (mt) REVERT: J 101 LEU cc_start: 0.8889 (tp) cc_final: 0.7974 (mt) REVERT: J 102 GLN cc_start: 0.8119 (mt0) cc_final: 0.7130 (mt0) REVERT: J 114 TYR cc_start: 0.6286 (m-10) cc_final: 0.5504 (m-10) REVERT: M 24 ARG cc_start: 0.7306 (mmm-85) cc_final: 0.6948 (mmm-85) REVERT: M 55 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7371 (tm-30) REVERT: M 69 THR cc_start: 0.8149 (p) cc_final: 0.7906 (p) REVERT: M 70 ASP cc_start: 0.7603 (t0) cc_final: 0.6856 (p0) REVERT: M 73 LEU cc_start: 0.7961 (tp) cc_final: 0.7439 (tp) REVERT: M 104 LEU cc_start: 0.7495 (tp) cc_final: 0.7058 (tp) REVERT: F 560 GLN cc_start: 0.9025 (tp40) cc_final: 0.8031 (tp40) REVERT: F 564 GLU cc_start: 0.8051 (mp0) cc_final: 0.7638 (mp0) REVERT: F 565 THR cc_start: 0.9301 (p) cc_final: 0.8987 (t) REVERT: S 4 LEU cc_start: 0.8438 (mt) cc_final: 0.8178 (mt) REVERT: S 78 ARG cc_start: 0.8441 (ttp-170) cc_final: 0.7909 (ttp-170) REVERT: S 96 LEU cc_start: 0.9338 (mp) cc_final: 0.9124 (tt) REVERT: P 15 SER cc_start: 0.8771 (m) cc_final: 0.7904 (p) REVERT: P 20 LEU cc_start: 0.9113 (mp) cc_final: 0.8815 (mp) REVERT: P 60 ASN cc_start: 0.9239 (t0) cc_final: 0.8899 (t0) outliers start: 0 outliers final: 0 residues processed: 565 average time/residue: 0.1338 time to fit residues: 116.7562 Evaluate side-chains 465 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 9.9990 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 203 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 208 optimal weight: 7.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** 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 N 76 ASN N 77 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN 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 27 GLN ** 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 = 0.3639 r_free = 0.3639 target = 0.107671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.077637 restraints weight = 54409.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.080041 restraints weight = 29789.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.081576 restraints weight = 20745.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.082452 restraints weight = 16684.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.083000 restraints weight = 14757.701| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19314 Z= 0.136 Angle : 0.715 10.586 26295 Z= 0.360 Chirality : 0.049 0.311 2952 Planarity : 0.004 0.076 3315 Dihedral : 6.226 37.103 3141 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.05 % Allowed : 0.15 % Favored : 99.80 % 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: -0.82 (0.18), residues: 2340 helix: 0.81 (0.38), residues: 180 sheet: -0.31 (0.18), residues: 867 loop : -0.86 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 172 TYR 0.038 0.002 TYR I 114 PHE 0.019 0.001 PHE A 252 TRP 0.024 0.001 TRP L 35 HIS 0.014 0.001 HIS O 52 Details of bonding type rmsd covalent geometry : bond 0.00308 (19266) covalent geometry : angle 0.69443 (26172) SS BOND : bond 0.00488 ( 21) SS BOND : angle 1.51159 ( 42) hydrogen bonds : bond 0.03409 ( 622) hydrogen bonds : angle 5.63843 ( 1749) link_ALPHA1-3 : bond 0.01193 ( 3) link_ALPHA1-3 : angle 1.40582 ( 9) link_ALPHA1-6 : bond 0.00620 ( 3) link_ALPHA1-6 : angle 1.63106 ( 9) link_BETA1-4 : bond 0.00496 ( 6) link_BETA1-4 : angle 2.76234 ( 18) link_NAG-ASN : bond 0.00625 ( 15) link_NAG-ASN : angle 3.51768 ( 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 555 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 554 time to evaluate : 0.610 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: A 62 GLN cc_start: 0.9066 (mt0) cc_final: 0.8625 (mt0) REVERT: A 78 ASP cc_start: 0.8160 (t70) cc_final: 0.7809 (t70) REVERT: A 272 LYS cc_start: 0.4706 (pttt) cc_final: 0.4484 (pttm) REVERT: H 59 PHE cc_start: 0.7091 (t80) cc_final: 0.6857 (t80) REVERT: H 60 TYR cc_start: 0.7799 (m-80) cc_final: 0.7485 (m-80) REVERT: H 101 LEU cc_start: 0.8843 (tp) cc_final: 0.8590 (tp) REVERT: H 114 TYR cc_start: 0.6158 (m-10) cc_final: 0.5752 (m-10) REVERT: K 81 GLU cc_start: 0.8707 (mp0) cc_final: 0.8469 (mp0) REVERT: D 512 ASN cc_start: 0.8914 (t0) cc_final: 0.8677 (t0) REVERT: D 560 GLN cc_start: 0.8836 (tp40) cc_final: 0.8088 (tm-30) REVERT: D 565 THR cc_start: 0.9252 (p) cc_final: 0.8961 (t) REVERT: D 578 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8223 (mm-30) REVERT: D 592 PHE cc_start: 0.8315 (t80) cc_final: 0.7990 (t80) REVERT: N 15 SER cc_start: 0.8572 (m) cc_final: 0.7335 (p) REVERT: B 47 ASP cc_start: 0.6778 (t0) cc_final: 0.6192 (t0) REVERT: B 62 GLN cc_start: 0.9151 (mt0) cc_final: 0.8677 (mt0) REVERT: B 117 ASP cc_start: 0.8711 (p0) cc_final: 0.8442 (p0) REVERT: I 31 ASN cc_start: 0.8625 (p0) cc_final: 0.7668 (m110) REVERT: I 46 GLU cc_start: 0.8627 (pt0) cc_final: 0.8269 (pm20) REVERT: I 59 PHE cc_start: 0.7150 (t80) cc_final: 0.6669 (t80) REVERT: I 83 MET cc_start: 0.8657 (mmm) cc_final: 0.7783 (mmm) REVERT: I 118 LEU cc_start: 0.8079 (tt) cc_final: 0.7716 (mm) REVERT: L 31 ASN cc_start: 0.7109 (p0) cc_final: 0.6826 (m-40) REVERT: L 55 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7206 (tm-30) REVERT: L 69 THR cc_start: 0.8387 (p) cc_final: 0.7964 (p) REVERT: L 70 ASP cc_start: 0.7286 (t0) cc_final: 0.6775 (p0) REVERT: E 514 ASN cc_start: 0.8999 (m-40) cc_final: 0.8451 (m-40) REVERT: E 555 ILE cc_start: 0.9135 (mt) cc_final: 0.8852 (mt) REVERT: E 560 GLN cc_start: 0.8884 (tp40) cc_final: 0.7462 (tp40) REVERT: E 564 GLU cc_start: 0.7791 (mp0) cc_final: 0.7482 (mp0) REVERT: E 565 THR cc_start: 0.9239 (p) cc_final: 0.8904 (t) REVERT: E 578 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8356 (mm-30) REVERT: E 579 LEU cc_start: 0.9118 (mm) cc_final: 0.8818 (tp) REVERT: E 581 THR cc_start: 0.9545 (m) cc_final: 0.9191 (p) REVERT: E 597 TRP cc_start: 0.7288 (t-100) cc_final: 0.7056 (t-100) REVERT: R 61 ASP cc_start: 0.8207 (p0) cc_final: 0.7776 (t0) REVERT: R 82 GLU cc_start: 0.8258 (pm20) cc_final: 0.7592 (pm20) REVERT: R 96 LEU cc_start: 0.9332 (mt) cc_final: 0.8975 (tt) REVERT: O 13 LYS cc_start: 0.8958 (tmmt) cc_final: 0.8540 (ttpp) REVERT: O 16 GLU cc_start: 0.8393 (pt0) cc_final: 0.7748 (pt0) REVERT: C 56 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7413 (mmmt) REVERT: C 62 GLN cc_start: 0.9065 (mt0) cc_final: 0.8577 (mt0) REVERT: J 12 VAL cc_start: 0.6820 (t) cc_final: 0.6448 (t) REVERT: J 46 GLU cc_start: 0.8801 (pt0) cc_final: 0.8420 (pm20) REVERT: J 59 PHE cc_start: 0.7293 (t80) cc_final: 0.6967 (t80) REVERT: J 80 TYR cc_start: 0.8100 (m-80) cc_final: 0.7842 (m-80) REVERT: J 101 LEU cc_start: 0.8851 (tp) cc_final: 0.7664 (mt) REVERT: J 102 GLN cc_start: 0.8109 (mt0) cc_final: 0.7112 (mt0) REVERT: J 114 TYR cc_start: 0.6251 (m-10) cc_final: 0.5487 (m-10) REVERT: J 115 TYR cc_start: 0.8713 (m-10) cc_final: 0.8466 (m-10) REVERT: M 17 ASP cc_start: 0.7429 (m-30) cc_final: 0.7222 (m-30) REVERT: M 24 ARG cc_start: 0.7339 (mmm-85) cc_final: 0.7012 (mmm-85) REVERT: M 31 ASN cc_start: 0.8177 (t0) cc_final: 0.7884 (t0) REVERT: M 55 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7482 (tm-30) REVERT: M 69 THR cc_start: 0.8161 (p) cc_final: 0.7879 (p) REVERT: M 70 ASP cc_start: 0.7582 (t0) cc_final: 0.6876 (p0) REVERT: M 73 LEU cc_start: 0.7954 (tp) cc_final: 0.7496 (tp) REVERT: M 104 LEU cc_start: 0.7653 (tp) cc_final: 0.7275 (tp) REVERT: F 560 GLN cc_start: 0.8886 (tp40) cc_final: 0.7996 (tp40) REVERT: F 564 GLU cc_start: 0.8036 (mp0) cc_final: 0.7442 (mp0) REVERT: F 565 THR cc_start: 0.9276 (p) cc_final: 0.8958 (t) REVERT: S 4 LEU cc_start: 0.8432 (mt) cc_final: 0.8168 (mt) REVERT: S 78 ARG cc_start: 0.8449 (ttp-170) cc_final: 0.8005 (ttp-170) REVERT: S 96 LEU cc_start: 0.9331 (mp) cc_final: 0.9092 (tt) REVERT: P 1 GLN cc_start: 0.6753 (mm-40) cc_final: 0.6444 (mm-40) REVERT: P 15 SER cc_start: 0.8782 (m) cc_final: 0.7903 (p) REVERT: P 20 LEU cc_start: 0.9036 (mp) cc_final: 0.8731 (mp) REVERT: P 60 ASN cc_start: 0.9204 (t0) cc_final: 0.8870 (t0) outliers start: 1 outliers final: 0 residues processed: 555 average time/residue: 0.1277 time to fit residues: 110.3226 Evaluate side-chains 463 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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: 1.9990 chunk 220 optimal weight: 7.9990 chunk 138 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** D 521 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 43 GLN O 76 ASN C 73 ASN ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN ** J 112 HIS ** 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 = 0.3628 r_free = 0.3628 target = 0.107000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076954 restraints weight = 54871.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.079281 restraints weight = 30406.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.080814 restraints weight = 21158.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.081734 restraints weight = 16993.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082230 restraints weight = 14973.803| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19314 Z= 0.158 Angle : 0.717 9.829 26295 Z= 0.359 Chirality : 0.048 0.313 2952 Planarity : 0.004 0.068 3315 Dihedral : 6.112 36.653 3141 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % 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: -0.82 (0.18), residues: 2340 helix: 0.80 (0.37), residues: 180 sheet: -0.44 (0.17), residues: 891 loop : -0.76 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 172 TYR 0.027 0.002 TYR I 114 PHE 0.022 0.002 PHE F 592 TRP 0.022 0.002 TRP L 35 HIS 0.012 0.001 HIS O 52 Details of bonding type rmsd covalent geometry : bond 0.00366 (19266) covalent geometry : angle 0.69608 (26172) SS BOND : bond 0.00660 ( 21) SS BOND : angle 1.50383 ( 42) hydrogen bonds : bond 0.03413 ( 622) hydrogen bonds : angle 5.53402 ( 1749) link_ALPHA1-3 : bond 0.01058 ( 3) link_ALPHA1-3 : angle 1.35340 ( 9) link_ALPHA1-6 : bond 0.00558 ( 3) link_ALPHA1-6 : angle 1.71286 ( 9) link_BETA1-4 : bond 0.00367 ( 6) link_BETA1-4 : angle 2.74709 ( 18) link_NAG-ASN : bond 0.00547 ( 15) link_NAG-ASN : angle 3.56632 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3760.29 seconds wall clock time: 65 minutes 46.19 seconds (3946.19 seconds total)