Starting phenix.real_space_refine on Wed Nov 19 00:28:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pci_20301/11_2025/6pci_20301.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pci_20301/11_2025/6pci_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_20301/11_2025/6pci_20301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pci_20301/11_2025/6pci_20301.map" model { file = "/net/cci-nas-00/data/ceres_data/6pci_20301/11_2025/6pci_20301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pci_20301/11_2025/6pci_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-2.0-5881/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: 4.08, per 1000 atoms: 0.22 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: 1.88 Conformation dependent library (CDL) restraints added in 923.9 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: 0.96 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: 4.06 Time building geometry restraints manager: 2.50 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.730 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.779 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: 0.8991 (mt0) cc_final: 0.8716 (mt0) REVERT: A 106 GLU cc_start: 0.8713 (tp30) cc_final: 0.7929 (tp30) REVERT: A 117 ASP cc_start: 0.8719 (p0) cc_final: 0.8375 (p0) REVERT: A 261 TYR cc_start: 0.7926 (m-10) cc_final: 0.7714 (m-10) REVERT: H 12 VAL cc_start: 0.6934 (t) cc_final: 0.6208 (t) REVERT: H 45 LEU cc_start: 0.7673 (tp) cc_final: 0.7320 (tp) REVERT: H 57 LYS cc_start: 0.8460 (tppt) cc_final: 0.8249 (tttm) REVERT: H 80 TYR cc_start: 0.8596 (m-10) cc_final: 0.8341 (m-80) REVERT: K 36 TYR cc_start: 0.8091 (m-10) cc_final: 0.7890 (m-80) REVERT: K 47 LEU cc_start: 0.9329 (mt) cc_final: 0.8917 (mt) REVERT: K 78 LEU cc_start: 0.7286 (mt) cc_final: 0.6774 (mt) REVERT: K 89 GLN cc_start: 0.8367 (tt0) cc_final: 0.7887 (tt0) REVERT: K 92 LYS cc_start: 0.8837 (tttt) cc_final: 0.8465 (tppt) REVERT: K 104 LEU cc_start: 0.7012 (tp) cc_final: 0.5620 (tp) REVERT: D 532 ILE cc_start: 0.9441 (mt) cc_final: 0.9155 (pt) REVERT: D 597 TRP cc_start: 0.7619 (t-100) cc_final: 0.7273 (t-100) REVERT: Q 20 THR cc_start: 0.8415 (p) cc_final: 0.7605 (p) REVERT: Q 38 GLN cc_start: 0.8945 (tt0) cc_final: 0.8672 (tt0) REVERT: Q 43 GLN cc_start: 0.8580 (mm-40) cc_final: 0.7906 (mm-40) REVERT: Q 54 THR cc_start: 0.9421 (m) cc_final: 0.9092 (p) REVERT: Q 79 LEU cc_start: 0.8430 (mt) cc_final: 0.7671 (mt) REVERT: N 77 GLN cc_start: 0.8462 (mt0) cc_final: 0.8161 (mt0) REVERT: N 100 TRP cc_start: 0.9136 (t-100) cc_final: 0.8790 (t-100) REVERT: B 62 GLN cc_start: 0.8966 (mt0) cc_final: 0.8709 (mt0) REVERT: B 106 GLU cc_start: 0.8685 (tp30) cc_final: 0.8075 (tp30) REVERT: B 117 ASP cc_start: 0.8801 (p0) cc_final: 0.8406 (p0) REVERT: B 178 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8722 (mt-10) REVERT: B 272 LYS cc_start: 0.6171 (pttt) cc_final: 0.5923 (pttm) REVERT: I 34 MET cc_start: 0.7829 (mmm) cc_final: 0.7551 (mmp) REVERT: I 45 LEU cc_start: 0.7841 (tp) cc_final: 0.7495 (tp) REVERT: I 57 LYS cc_start: 0.8529 (tppt) cc_final: 0.8307 (tttm) REVERT: I 64 VAL cc_start: 0.9132 (m) cc_final: 0.8480 (t) REVERT: I 80 TYR cc_start: 0.8695 (m-10) cc_final: 0.8437 (m-80) REVERT: I 94 TYR cc_start: 0.7281 (m-10) cc_final: 0.6777 (m-10) REVERT: I 112 HIS cc_start: 0.6153 (t-90) cc_final: 0.5644 (t-90) REVERT: L 36 TYR cc_start: 0.8168 (m-10) cc_final: 0.7951 (m-80) REVERT: L 73 LEU cc_start: 0.8171 (tp) cc_final: 0.7895 (tp) REVERT: L 89 GLN cc_start: 0.8353 (tt0) cc_final: 0.8122 (tt0) REVERT: L 92 LYS cc_start: 0.8862 (tttt) cc_final: 0.8329 (tppt) REVERT: E 532 ILE cc_start: 0.9454 (mt) cc_final: 0.9115 (pt) REVERT: E 555 ILE cc_start: 0.9017 (mt) cc_final: 0.8761 (mp) REVERT: E 597 TRP cc_start: 0.7706 (t-100) cc_final: 0.7349 (t-100) REVERT: R 13 LEU cc_start: 0.8493 (mp) cc_final: 0.8282 (mp) REVERT: R 34 PHE cc_start: 0.8449 (m-10) cc_final: 0.7829 (m-10) REVERT: R 61 ASP cc_start: 0.8457 (p0) cc_final: 0.8083 (t0) REVERT: O 35 ASN cc_start: 0.8771 (m-40) cc_final: 0.8431 (m-40) REVERT: O 58 ASN cc_start: 0.8739 (t0) cc_final: 0.8521 (t0) REVERT: O 100 TRP cc_start: 0.9169 (t-100) cc_final: 0.8494 (t-100) REVERT: C 62 GLN cc_start: 0.8834 (mt0) cc_final: 0.8567 (mt0) REVERT: C 78 ASP cc_start: 0.8116 (t0) cc_final: 0.7888 (t0) REVERT: C 106 GLU cc_start: 0.8658 (tp30) cc_final: 0.7901 (tp30) REVERT: C 117 ASP cc_start: 0.8791 (p0) cc_final: 0.8391 (p0) REVERT: C 163 ASP cc_start: 0.9356 (t0) cc_final: 0.9095 (t0) REVERT: J 12 VAL cc_start: 0.6382 (t) cc_final: 0.6076 (t) REVERT: J 36 TRP cc_start: 0.6993 (m100) cc_final: 0.5899 (m100) REVERT: J 46 GLU cc_start: 0.8743 (pt0) cc_final: 0.8225 (pm20) REVERT: J 57 LYS cc_start: 0.8649 (tppt) cc_final: 0.8233 (tttm) REVERT: J 64 VAL cc_start: 0.9160 (m) cc_final: 0.8607 (t) REVERT: J 80 TYR cc_start: 0.8689 (m-10) cc_final: 0.8335 (m-80) REVERT: J 83 MET cc_start: 0.8598 (mtt) cc_final: 0.8365 (mmm) REVERT: J 102 GLN cc_start: 0.8058 (mt0) cc_final: 0.7554 (mt0) REVERT: M 31 ASN cc_start: 0.7171 (p0) cc_final: 0.6783 (m-40) REVERT: M 37 GLN cc_start: 0.7919 (tt0) cc_final: 0.7697 (tt0) REVERT: M 58 VAL cc_start: 0.7347 (t) cc_final: 0.7052 (p) REVERT: M 73 LEU cc_start: 0.7992 (tp) cc_final: 0.7623 (tp) REVERT: M 85 THR cc_start: 0.6511 (m) cc_final: 0.6309 (p) REVERT: M 86 TYR cc_start: 0.6745 (m-10) cc_final: 0.6206 (m-80) REVERT: M 92 LYS cc_start: 0.8977 (tttt) cc_final: 0.8521 (ttmm) REVERT: F 581 THR cc_start: 0.9623 (m) cc_final: 0.9032 (p) REVERT: S 20 THR cc_start: 0.8465 (p) cc_final: 0.7756 (p) REVERT: S 21 LEU cc_start: 0.8399 (tp) cc_final: 0.8158 (tp) REVERT: S 34 PHE cc_start: 0.7778 (m-10) cc_final: 0.7389 (m-10) REVERT: S 47 LEU cc_start: 0.9025 (tp) cc_final: 0.8807 (tt) REVERT: S 61 ASP cc_start: 0.8279 (p0) cc_final: 0.7805 (t0) REVERT: S 78 ARG cc_start: 0.8642 (mmm160) cc_final: 0.8440 (ttp-170) REVERT: S 84 PHE cc_start: 0.7584 (t80) cc_final: 0.7117 (t80) REVERT: S 97 TYR cc_start: 0.8644 (m-80) cc_final: 0.8429 (m-80) REVERT: P 60 ASN cc_start: 0.9117 (t0) cc_final: 0.8650 (t0) REVERT: P 100 TRP cc_start: 0.9135 (t-100) cc_final: 0.8695 (t-100) REVERT: P 112 ASP cc_start: 0.8943 (p0) cc_final: 0.8268 (p0) outliers start: 0 outliers final: 0 residues processed: 774 average time/residue: 0.1759 time to fit residues: 194.8142 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 : 0.767 ------------------------------------------------------------------------------- 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 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 ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN C 188 GLN C 255 GLN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN S 43 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.108363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.078632 restraints weight = 54021.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.081710 restraints weight = 30276.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082280 restraints weight = 19275.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.082731 restraints weight = 16225.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.082822 restraints weight = 15246.895| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19314 Z= 0.155 Angle : 0.729 9.913 26295 Z= 0.373 Chirality : 0.050 0.391 2952 Planarity : 0.005 0.038 3315 Dihedral : 9.577 75.219 3141 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % 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: -0.86 (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 0.018 0.001 TRP A 104 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00333 (19266) covalent geometry : angle 0.69961 (26172) SS BOND : bond 0.00407 ( 21) SS BOND : angle 1.08026 ( 42) hydrogen bonds : bond 0.04576 ( 622) hydrogen bonds : angle 7.37286 ( 1749) link_ALPHA1-3 : bond 0.01147 ( 3) link_ALPHA1-3 : angle 2.10510 ( 9) link_ALPHA1-6 : bond 0.00469 ( 3) link_ALPHA1-6 : angle 1.95317 ( 9) link_BETA1-4 : bond 0.00313 ( 6) link_BETA1-4 : angle 3.31196 ( 18) link_NAG-ASN : bond 0.00655 ( 15) link_NAG-ASN : angle 4.32248 ( 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 706 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 706 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9246 (mt0) cc_final: 0.8910 (mt0) REVERT: A 78 ASP cc_start: 0.8221 (t70) cc_final: 0.7916 (t70) REVERT: A 117 ASP cc_start: 0.8586 (p0) cc_final: 0.8274 (p0) REVERT: A 150 ASP cc_start: 0.8722 (m-30) cc_final: 0.8514 (m-30) REVERT: A 272 LYS cc_start: 0.5745 (pttt) cc_final: 0.5392 (ttmm) REVERT: H 12 VAL cc_start: 0.7017 (t) cc_final: 0.6487 (t) REVERT: H 45 LEU cc_start: 0.7604 (tp) cc_final: 0.7325 (tp) REVERT: H 86 LEU cc_start: 0.9147 (mt) cc_final: 0.8915 (mt) REVERT: K 46 LEU cc_start: 0.9022 (pt) cc_final: 0.8820 (pt) REVERT: K 81 GLU cc_start: 0.8688 (mp0) cc_final: 0.8367 (mp0) REVERT: K 82 ASP cc_start: 0.6871 (m-30) cc_final: 0.6261 (t0) REVERT: K 86 TYR cc_start: 0.6090 (m-10) cc_final: 0.3899 (m-10) REVERT: K 106 ILE cc_start: 0.2697 (mm) cc_final: 0.2420 (mm) REVERT: D 532 ILE cc_start: 0.9305 (mt) cc_final: 0.9083 (pt) REVERT: D 560 GLN cc_start: 0.9231 (tp40) cc_final: 0.8437 (tp40) REVERT: D 581 THR cc_start: 0.9608 (m) cc_final: 0.9364 (p) REVERT: D 592 PHE cc_start: 0.8453 (t80) cc_final: 0.8011 (t80) REVERT: Q 4 LEU cc_start: 0.8729 (mt) cc_final: 0.8523 (mt) REVERT: Q 21 LEU cc_start: 0.8305 (tp) cc_final: 0.7973 (tp) REVERT: Q 61 ASP cc_start: 0.8068 (p0) cc_final: 0.7780 (p0) REVERT: N 15 SER cc_start: 0.8826 (m) cc_final: 0.8550 (p) REVERT: N 100 TRP cc_start: 0.9092 (t-100) cc_final: 0.8618 (t-100) REVERT: N 112 ASP cc_start: 0.8990 (p0) cc_final: 0.8539 (p0) REVERT: B 62 GLN cc_start: 0.9287 (mt0) cc_final: 0.8514 (mt0) REVERT: B 103 GLU cc_start: 0.8261 (tt0) cc_final: 0.7897 (tt0) REVERT: B 117 ASP cc_start: 0.8610 (p0) cc_final: 0.8207 (p0) REVERT: B 156 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7647 (mt-10) REVERT: I 34 MET cc_start: 0.7681 (mmm) cc_final: 0.7466 (mmp) REVERT: I 46 GLU cc_start: 0.8619 (pt0) cc_final: 0.8267 (pm20) REVERT: I 86 LEU cc_start: 0.9083 (mt) cc_final: 0.8821 (mt) REVERT: L 31 ASN cc_start: 0.7071 (p0) cc_final: 0.6417 (m-40) REVERT: L 36 TYR cc_start: 0.8306 (m-10) cc_final: 0.8040 (m-80) REVERT: L 73 LEU cc_start: 0.8341 (tp) cc_final: 0.8063 (tp) REVERT: L 89 GLN cc_start: 0.8284 (tt0) cc_final: 0.7987 (tt0) REVERT: L 90 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7103 (tp40) REVERT: E 532 ILE cc_start: 0.9304 (mt) cc_final: 0.9033 (pt) REVERT: E 534 TYR cc_start: 0.9288 (t80) cc_final: 0.9013 (t80) REVERT: E 573 LEU cc_start: 0.9602 (mt) cc_final: 0.9347 (mt) REVERT: E 581 THR cc_start: 0.9662 (m) cc_final: 0.9292 (p) REVERT: E 597 TRP cc_start: 0.7495 (t-100) cc_final: 0.7263 (t-100) REVERT: R 13 LEU cc_start: 0.8451 (mp) cc_final: 0.8227 (mp) REVERT: R 18 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7769 (ttp80) REVERT: R 21 LEU cc_start: 0.8001 (tt) cc_final: 0.7565 (mm) REVERT: R 36 TRP cc_start: 0.8540 (m100) cc_final: 0.8261 (m100) REVERT: R 61 ASP cc_start: 0.8308 (p0) cc_final: 0.8064 (t0) REVERT: O 58 ASN cc_start: 0.8728 (t0) cc_final: 0.8227 (t0) REVERT: O 100 TRP cc_start: 0.9112 (t-100) cc_final: 0.8644 (t-100) REVERT: C 62 GLN cc_start: 0.9311 (mt0) cc_final: 0.8398 (mt0) REVERT: C 68 LEU cc_start: 0.9428 (mt) cc_final: 0.9209 (mt) REVERT: C 117 ASP cc_start: 0.8558 (p0) cc_final: 0.8306 (p0) REVERT: C 273 LEU cc_start: 0.7657 (mp) cc_final: 0.7288 (mp) REVERT: J 12 VAL cc_start: 0.6773 (t) cc_final: 0.6453 (t) REVERT: J 36 TRP cc_start: 0.6880 (m100) cc_final: 0.5897 (m100) REVERT: J 46 GLU cc_start: 0.8760 (pt0) cc_final: 0.8314 (pm20) REVERT: J 57 LYS cc_start: 0.8841 (tppt) cc_final: 0.8450 (tttm) REVERT: J 83 MET cc_start: 0.8789 (mtt) cc_final: 0.8386 (mmm) REVERT: J 102 GLN cc_start: 0.8181 (mt0) cc_final: 0.7718 (mt0) REVERT: J 128 THR cc_start: 0.9142 (m) cc_final: 0.8812 (t) REVERT: M 31 ASN cc_start: 0.7203 (p0) cc_final: 0.6896 (m-40) REVERT: M 58 VAL cc_start: 0.7198 (t) cc_final: 0.6915 (p) REVERT: M 73 LEU cc_start: 0.8142 (tp) cc_final: 0.7655 (tp) REVERT: M 86 TYR cc_start: 0.6415 (m-10) cc_final: 0.6001 (m-80) REVERT: M 89 GLN cc_start: 0.7551 (tt0) cc_final: 0.7316 (tt0) REVERT: M 90 GLN cc_start: 0.7756 (tp40) cc_final: 0.7313 (tp40) REVERT: M 104 LEU cc_start: 0.7685 (tp) cc_final: 0.6535 (tp) REVERT: F 581 THR cc_start: 0.9651 (m) cc_final: 0.9360 (p) REVERT: S 4 LEU cc_start: 0.8698 (mt) cc_final: 0.8314 (mt) REVERT: S 43 GLN cc_start: 0.8509 (mp10) cc_final: 0.8305 (mp10) REVERT: S 61 ASP cc_start: 0.8165 (p0) cc_final: 0.7790 (t0) REVERT: P 15 SER cc_start: 0.8946 (m) cc_final: 0.8450 (p) REVERT: P 32 TYR cc_start: 0.8789 (m-10) cc_final: 0.8226 (m-10) REVERT: P 60 ASN cc_start: 0.9210 (t0) cc_final: 0.8718 (t0) REVERT: P 100 TRP cc_start: 0.9075 (t-100) cc_final: 0.8656 (t-100) REVERT: P 111 MET cc_start: 0.8511 (mtm) cc_final: 0.8160 (mtt) outliers start: 0 outliers final: 0 residues processed: 706 average time/residue: 0.1431 time to fit residues: 152.4845 Evaluate side-chains 501 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 102 GLN ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN M 90 GLN ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.104393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.074022 restraints weight = 54964.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.076351 restraints weight = 30207.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077808 restraints weight = 21112.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.078661 restraints weight = 17097.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.079201 restraints weight = 15169.335| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 19314 Z= 0.278 Angle : 0.788 12.290 26295 Z= 0.396 Chirality : 0.050 0.395 2952 Planarity : 0.005 0.051 3315 Dihedral : 9.059 67.711 3141 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % 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: -1.56 (0.17), residues: 2340 helix: 0.12 (0.36), residues: 183 sheet: -1.17 (0.16), residues: 939 loop : -0.99 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 38 TYR 0.026 0.002 TYR H 114 PHE 0.014 0.002 PHE B 88 TRP 0.017 0.002 TRP O 114 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00631 (19266) covalent geometry : angle 0.75776 (26172) SS BOND : bond 0.00556 ( 21) SS BOND : angle 1.25203 ( 42) hydrogen bonds : bond 0.04340 ( 622) hydrogen bonds : angle 6.71316 ( 1749) link_ALPHA1-3 : bond 0.01537 ( 3) link_ALPHA1-3 : angle 1.84576 ( 9) link_ALPHA1-6 : bond 0.00114 ( 3) link_ALPHA1-6 : angle 2.18831 ( 9) link_BETA1-4 : bond 0.00532 ( 6) link_BETA1-4 : angle 3.08602 ( 18) link_NAG-ASN : bond 0.00547 ( 15) link_NAG-ASN : angle 4.65453 ( 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 589 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 588 time to evaluate : 0.778 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: A 39 HIS cc_start: 0.8266 (t70) cc_final: 0.7984 (t70) REVERT: A 62 GLN cc_start: 0.9259 (mt0) cc_final: 0.8749 (mt0) REVERT: A 78 ASP cc_start: 0.8375 (t70) cc_final: 0.8121 (t70) REVERT: A 117 ASP cc_start: 0.8440 (p0) cc_final: 0.8192 (p0) REVERT: H 36 TRP cc_start: 0.6794 (m100) cc_final: 0.6067 (m100) REVERT: H 102 GLN cc_start: 0.8390 (mt0) cc_final: 0.7657 (mt0) REVERT: H 114 TYR cc_start: 0.6512 (m-10) cc_final: 0.6067 (m-10) REVERT: K 46 LEU cc_start: 0.9118 (pt) cc_final: 0.8899 (pt) REVERT: K 81 GLU cc_start: 0.8629 (mp0) cc_final: 0.8259 (mp0) REVERT: D 512 ASN cc_start: 0.9350 (t0) cc_final: 0.9074 (t0) REVERT: D 581 THR cc_start: 0.9643 (m) cc_final: 0.9311 (p) REVERT: D 592 PHE cc_start: 0.8434 (t80) cc_final: 0.8037 (t80) REVERT: Q 61 ASP cc_start: 0.8193 (p0) cc_final: 0.7907 (p0) REVERT: N 15 SER cc_start: 0.8794 (m) cc_final: 0.8511 (p) REVERT: N 112 ASP cc_start: 0.9000 (p0) cc_final: 0.8703 (p0) REVERT: B 62 GLN cc_start: 0.9328 (mt0) cc_final: 0.8526 (mt0) REVERT: B 117 ASP cc_start: 0.8513 (p0) cc_final: 0.8109 (p0) REVERT: I 46 GLU cc_start: 0.8715 (pt0) cc_final: 0.8324 (pm20) REVERT: I 59 PHE cc_start: 0.7236 (t80) cc_final: 0.6701 (t80) REVERT: I 76 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8424 (ptpp) REVERT: I 80 TYR cc_start: 0.8389 (m-80) cc_final: 0.7433 (m-80) REVERT: I 86 LEU cc_start: 0.9255 (mt) cc_final: 0.8866 (mt) REVERT: L 31 ASN cc_start: 0.7300 (p0) cc_final: 0.6690 (m-40) REVERT: L 73 LEU cc_start: 0.8441 (tp) cc_final: 0.8094 (tp) REVERT: L 89 GLN cc_start: 0.8356 (tt0) cc_final: 0.7977 (tt0) REVERT: L 93 SER cc_start: 0.8615 (p) cc_final: 0.8402 (t) REVERT: E 532 ILE cc_start: 0.9383 (mt) cc_final: 0.9162 (pt) REVERT: E 555 ILE cc_start: 0.9191 (mt) cc_final: 0.8907 (mt) REVERT: E 565 THR cc_start: 0.9244 (p) cc_final: 0.8822 (t) REVERT: E 581 THR cc_start: 0.9649 (m) cc_final: 0.9300 (p) REVERT: E 597 TRP cc_start: 0.7670 (t-100) cc_final: 0.7374 (t-100) REVERT: R 61 ASP cc_start: 0.8333 (p0) cc_final: 0.8022 (t0) REVERT: O 35 ASN cc_start: 0.8780 (m-40) cc_final: 0.8266 (m-40) REVERT: O 111 MET cc_start: 0.8307 (mtt) cc_final: 0.8026 (mtt) REVERT: C 62 GLN cc_start: 0.9145 (mt0) cc_final: 0.8521 (mt0) REVERT: C 68 LEU cc_start: 0.9495 (mt) cc_final: 0.9180 (mt) REVERT: C 117 ASP cc_start: 0.8352 (p0) cc_final: 0.8135 (p0) REVERT: J 12 VAL cc_start: 0.6864 (t) cc_final: 0.6543 (t) REVERT: J 31 ASN cc_start: 0.8246 (t0) cc_final: 0.8013 (t0) REVERT: J 46 GLU cc_start: 0.8699 (pt0) cc_final: 0.8278 (pm20) REVERT: J 82 GLN cc_start: 0.8110 (tp40) cc_final: 0.7850 (tp-100) REVERT: J 83 MET cc_start: 0.8654 (mtt) cc_final: 0.8392 (mmm) REVERT: J 101 LEU cc_start: 0.9096 (tp) cc_final: 0.8888 (tp) REVERT: J 102 GLN cc_start: 0.8248 (mt0) cc_final: 0.7976 (mt0) REVERT: J 128 THR cc_start: 0.9338 (m) cc_final: 0.9055 (t) REVERT: M 31 ASN cc_start: 0.7324 (p0) cc_final: 0.7106 (m-40) REVERT: M 58 VAL cc_start: 0.7681 (t) cc_final: 0.7289 (p) REVERT: M 73 LEU cc_start: 0.8113 (tp) cc_final: 0.7716 (tp) REVERT: M 90 GLN cc_start: 0.8206 (tp-100) cc_final: 0.7484 (tp40) REVERT: F 581 THR cc_start: 0.9665 (m) cc_final: 0.9323 (p) REVERT: F 592 PHE cc_start: 0.8248 (t80) cc_final: 0.7879 (t80) REVERT: S 4 LEU cc_start: 0.8499 (mt) cc_final: 0.8232 (mt) REVERT: S 61 ASP cc_start: 0.8233 (p0) cc_final: 0.7789 (t0) REVERT: P 15 SER cc_start: 0.8881 (m) cc_final: 0.8276 (p) REVERT: P 32 TYR cc_start: 0.8851 (m-10) cc_final: 0.8547 (m-10) REVERT: P 52 HIS cc_start: 0.7981 (t-90) cc_final: 0.7482 (t-90) REVERT: P 60 ASN cc_start: 0.9280 (t0) cc_final: 0.8883 (t0) REVERT: P 111 MET cc_start: 0.8669 (mtm) cc_final: 0.8198 (mtt) outliers start: 1 outliers final: 0 residues processed: 589 average time/residue: 0.1519 time to fit residues: 134.6459 Evaluate side-chains 461 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 63 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 D 508 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN I 102 GLN E 508 GLN E 567 GLN ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN S 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.106356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.076217 restraints weight = 54260.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078639 restraints weight = 29360.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.080191 restraints weight = 20242.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.081114 restraints weight = 16198.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.081535 restraints weight = 14253.299| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19314 Z= 0.165 Angle : 0.698 10.324 26295 Z= 0.352 Chirality : 0.049 0.358 2952 Planarity : 0.004 0.053 3315 Dihedral : 8.088 56.066 3141 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.20 % Allowed : 2.56 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2340 helix: 0.57 (0.37), residues: 183 sheet: -0.70 (0.17), residues: 885 loop : -0.96 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 52 TYR 0.020 0.002 TYR P 107 PHE 0.017 0.002 PHE F 582 TRP 0.014 0.001 TRP P 114 HIS 0.006 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00373 (19266) covalent geometry : angle 0.67124 (26172) SS BOND : bond 0.00551 ( 21) SS BOND : angle 1.02945 ( 42) hydrogen bonds : bond 0.03695 ( 622) hydrogen bonds : angle 6.15837 ( 1749) link_ALPHA1-3 : bond 0.00692 ( 3) link_ALPHA1-3 : angle 1.51827 ( 9) link_ALPHA1-6 : bond 0.00215 ( 3) link_ALPHA1-6 : angle 1.98389 ( 9) link_BETA1-4 : bond 0.00408 ( 6) link_BETA1-4 : angle 3.04549 ( 18) link_NAG-ASN : bond 0.00520 ( 15) link_NAG-ASN : angle 4.11966 ( 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 610 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 606 time to evaluate : 0.797 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 39 HIS cc_start: 0.8295 (t70) cc_final: 0.8079 (t70) REVERT: A 62 GLN cc_start: 0.9302 (mt0) cc_final: 0.8640 (mt0) REVERT: A 78 ASP cc_start: 0.8305 (t70) cc_final: 0.8099 (t70) REVERT: A 117 ASP cc_start: 0.8377 (p0) cc_final: 0.8007 (p0) REVERT: H 52 ARG cc_start: 0.8658 (mtm-85) cc_final: 0.8356 (mtm-85) REVERT: H 114 TYR cc_start: 0.6324 (m-10) cc_final: 0.5762 (m-10) REVERT: H 115 TYR cc_start: 0.8717 (m-10) cc_final: 0.8455 (m-10) REVERT: K 46 LEU cc_start: 0.9094 (pt) cc_final: 0.8864 (pt) REVERT: K 81 GLU cc_start: 0.8598 (mp0) cc_final: 0.8286 (mp0) REVERT: K 89 GLN cc_start: 0.8420 (tt0) cc_final: 0.8136 (tt0) REVERT: D 565 THR cc_start: 0.9224 (p) cc_final: 0.8852 (t) REVERT: D 579 LEU cc_start: 0.8865 (mm) cc_final: 0.8489 (tp) REVERT: D 581 THR cc_start: 0.9606 (m) cc_final: 0.9311 (p) REVERT: Q 61 ASP cc_start: 0.8063 (p0) cc_final: 0.7849 (p0) REVERT: N 15 SER cc_start: 0.8657 (m) cc_final: 0.8350 (p) REVERT: N 52 HIS cc_start: 0.7843 (t-90) cc_final: 0.7115 (t-90) REVERT: B 47 ASP cc_start: 0.6403 (t0) cc_final: 0.6049 (t0) REVERT: B 62 GLN cc_start: 0.9130 (mt0) cc_final: 0.8420 (mt0) REVERT: B 117 ASP cc_start: 0.8551 (p0) cc_final: 0.8213 (p0) REVERT: I 28 MET cc_start: 0.7118 (tmm) cc_final: 0.6773 (tmm) REVERT: I 46 GLU cc_start: 0.8629 (pt0) cc_final: 0.8218 (pm20) REVERT: I 48 MET cc_start: 0.8394 (mmm) cc_final: 0.7849 (tpp) REVERT: I 59 PHE cc_start: 0.7389 (t80) cc_final: 0.7060 (t80) REVERT: I 76 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8389 (ptpp) REVERT: I 80 TYR cc_start: 0.8250 (m-80) cc_final: 0.7039 (m-80) REVERT: I 86 LEU cc_start: 0.9134 (mt) cc_final: 0.8931 (mt) REVERT: L 31 ASN cc_start: 0.7230 (p0) cc_final: 0.6626 (m-40) REVERT: L 73 LEU cc_start: 0.8374 (tp) cc_final: 0.8014 (tp) REVERT: L 104 LEU cc_start: 0.7744 (tp) cc_final: 0.7265 (tt) REVERT: E 532 ILE cc_start: 0.9236 (mt) cc_final: 0.8912 (pt) REVERT: E 555 ILE cc_start: 0.9125 (mt) cc_final: 0.8864 (mt) REVERT: E 565 THR cc_start: 0.9159 (p) cc_final: 0.8759 (t) REVERT: E 573 LEU cc_start: 0.9634 (mt) cc_final: 0.9379 (mm) REVERT: E 581 THR cc_start: 0.9611 (m) cc_final: 0.9346 (p) REVERT: R 61 ASP cc_start: 0.8284 (p0) cc_final: 0.7941 (t0) REVERT: O 16 GLU cc_start: 0.8572 (pt0) cc_final: 0.8175 (pt0) REVERT: C 62 GLN cc_start: 0.9056 (mt0) cc_final: 0.8348 (mt0) REVERT: C 68 LEU cc_start: 0.9400 (mt) cc_final: 0.9094 (mt) REVERT: C 172 ARG cc_start: 0.8685 (ttm110) cc_final: 0.8051 (ttm110) REVERT: J 12 VAL cc_start: 0.7048 (t) cc_final: 0.6742 (t) REVERT: J 35 HIS cc_start: 0.8185 (m-70) cc_final: 0.7884 (m90) REVERT: J 36 TRP cc_start: 0.7196 (m100) cc_final: 0.6848 (m100) REVERT: J 43 LYS cc_start: 0.8403 (mppt) cc_final: 0.8187 (mppt) REVERT: J 46 GLU cc_start: 0.8819 (pt0) cc_final: 0.8447 (pm20) REVERT: J 83 MET cc_start: 0.8620 (mtt) cc_final: 0.8399 (mmm) REVERT: J 102 GLN cc_start: 0.8332 (mt0) cc_final: 0.7892 (mt0) REVERT: J 128 THR cc_start: 0.9303 (m) cc_final: 0.9057 (t) REVERT: M 24 ARG cc_start: 0.7384 (mmm-85) cc_final: 0.6991 (mmm-85) REVERT: M 73 LEU cc_start: 0.8048 (tp) cc_final: 0.7556 (tp) REVERT: M 90 GLN cc_start: 0.7908 (tp-100) cc_final: 0.7309 (tp40) REVERT: F 581 THR cc_start: 0.9624 (m) cc_final: 0.9317 (p) REVERT: F 592 PHE cc_start: 0.8272 (t80) cc_final: 0.7822 (t80) REVERT: S 4 LEU cc_start: 0.8427 (mt) cc_final: 0.8149 (mt) REVERT: P 15 SER cc_start: 0.8914 (m) cc_final: 0.8339 (p) REVERT: P 32 TYR cc_start: 0.8784 (m-10) cc_final: 0.8499 (m-10) REVERT: P 52 HIS cc_start: 0.7890 (t-90) cc_final: 0.7464 (t-90) REVERT: P 60 ASN cc_start: 0.9284 (t0) cc_final: 0.8844 (t0) REVERT: P 111 MET cc_start: 0.8459 (mtm) cc_final: 0.8091 (mtp) outliers start: 4 outliers final: 0 residues processed: 610 average time/residue: 0.1511 time to fit residues: 138.6035 Evaluate side-chains 477 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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: 10.0000 chunk 170 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 74 ASN ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN N 77 GLN B 255 GLN I 31 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 567 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.106531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076464 restraints weight = 54032.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.078810 restraints weight = 29597.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.080315 restraints weight = 20569.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.081190 restraints weight = 16566.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.081750 restraints weight = 14592.385| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19314 Z= 0.169 Angle : 0.700 10.181 26295 Z= 0.350 Chirality : 0.049 0.328 2952 Planarity : 0.004 0.044 3315 Dihedral : 7.557 47.690 3141 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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 (0.18), residues: 2340 helix: 0.58 (0.38), residues: 180 sheet: -0.56 (0.17), residues: 894 loop : -0.98 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 18 TYR 0.025 0.002 TYR I 114 PHE 0.021 0.002 PHE D 592 TRP 0.012 0.001 TRP P 114 HIS 0.004 0.001 HIS I 112 Details of bonding type rmsd covalent geometry : bond 0.00385 (19266) covalent geometry : angle 0.67230 (26172) SS BOND : bond 0.00617 ( 21) SS BOND : angle 1.39331 ( 42) hydrogen bonds : bond 0.03558 ( 622) hydrogen bonds : angle 5.95537 ( 1749) link_ALPHA1-3 : bond 0.01053 ( 3) link_ALPHA1-3 : angle 1.74855 ( 9) link_ALPHA1-6 : bond 0.00254 ( 3) link_ALPHA1-6 : angle 1.92554 ( 9) link_BETA1-4 : bond 0.00429 ( 6) link_BETA1-4 : angle 2.96543 ( 18) link_NAG-ASN : bond 0.00551 ( 15) link_NAG-ASN : angle 4.04393 ( 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 584 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 0.744 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 39 HIS cc_start: 0.8332 (t70) cc_final: 0.8129 (t70) REVERT: A 62 GLN cc_start: 0.9299 (mt0) cc_final: 0.8669 (mt0) REVERT: A 117 ASP cc_start: 0.8507 (p0) cc_final: 0.8140 (p0) REVERT: H 52 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8330 (mtm-85) REVERT: H 57 LYS cc_start: 0.9283 (tptt) cc_final: 0.8832 (tttm) REVERT: H 114 TYR cc_start: 0.6269 (m-10) cc_final: 0.5842 (m-10) REVERT: H 115 TYR cc_start: 0.8795 (m-10) cc_final: 0.8561 (m-10) REVERT: K 46 LEU cc_start: 0.9086 (pt) cc_final: 0.8842 (pt) REVERT: K 81 GLU cc_start: 0.8648 (mp0) cc_final: 0.8383 (mp0) REVERT: K 89 GLN cc_start: 0.8416 (tt0) cc_final: 0.8167 (tt0) REVERT: D 512 ASN cc_start: 0.9195 (t0) cc_final: 0.8919 (t0) REVERT: D 560 GLN cc_start: 0.8818 (tp40) cc_final: 0.8497 (tp40) REVERT: D 565 THR cc_start: 0.9197 (p) cc_final: 0.8860 (t) REVERT: D 581 THR cc_start: 0.9632 (m) cc_final: 0.9348 (p) REVERT: D 592 PHE cc_start: 0.8491 (t80) cc_final: 0.8287 (t80) REVERT: Q 61 ASP cc_start: 0.8021 (p0) cc_final: 0.7804 (p0) REVERT: N 15 SER cc_start: 0.8616 (m) cc_final: 0.7823 (p) REVERT: N 52 HIS cc_start: 0.7882 (t-90) cc_final: 0.7110 (t-90) REVERT: B 47 ASP cc_start: 0.6507 (t0) cc_final: 0.6164 (t0) REVERT: B 62 GLN cc_start: 0.9098 (mt0) cc_final: 0.8552 (mt0) REVERT: B 117 ASP cc_start: 0.8636 (p0) cc_final: 0.8369 (p0) REVERT: B 240 THR cc_start: 0.9546 (m) cc_final: 0.9291 (p) REVERT: I 46 GLU cc_start: 0.8640 (pt0) cc_final: 0.8180 (pm20) REVERT: I 48 MET cc_start: 0.8385 (mmm) cc_final: 0.7885 (tpp) REVERT: I 59 PHE cc_start: 0.7359 (t80) cc_final: 0.6952 (t80) REVERT: I 76 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8416 (ptpp) REVERT: I 80 TYR cc_start: 0.8261 (m-80) cc_final: 0.7336 (m-80) REVERT: L 31 ASN cc_start: 0.7209 (p0) cc_final: 0.6827 (m-40) REVERT: L 70 ASP cc_start: 0.7204 (t0) cc_final: 0.6547 (p0) REVERT: L 73 LEU cc_start: 0.8348 (tp) cc_final: 0.7986 (tp) REVERT: L 104 LEU cc_start: 0.7639 (tp) cc_final: 0.7282 (tt) REVERT: E 514 ASN cc_start: 0.9167 (m-40) cc_final: 0.8808 (m110) REVERT: E 547 LEU cc_start: 0.9090 (mp) cc_final: 0.8786 (mp) REVERT: E 555 ILE cc_start: 0.9159 (mt) cc_final: 0.8843 (mt) REVERT: E 564 GLU cc_start: 0.7811 (mp0) cc_final: 0.7530 (mp0) REVERT: E 565 THR cc_start: 0.9152 (p) cc_final: 0.8773 (t) REVERT: E 581 THR cc_start: 0.9620 (m) cc_final: 0.9345 (p) REVERT: E 597 TRP cc_start: 0.7392 (t-100) cc_final: 0.7125 (t-100) REVERT: R 61 ASP cc_start: 0.8301 (p0) cc_final: 0.7950 (t0) REVERT: C 62 GLN cc_start: 0.9041 (mt0) cc_final: 0.8485 (mt0) REVERT: C 68 LEU cc_start: 0.9324 (mt) cc_final: 0.9086 (mt) REVERT: C 117 ASP cc_start: 0.8510 (p0) cc_final: 0.8235 (p0) REVERT: C 172 ARG cc_start: 0.8675 (ttm110) cc_final: 0.8086 (ttm110) REVERT: J 12 VAL cc_start: 0.6883 (t) cc_final: 0.6608 (t) REVERT: J 35 HIS cc_start: 0.8044 (m-70) cc_final: 0.7794 (m90) REVERT: J 43 LYS cc_start: 0.8430 (mppt) cc_final: 0.8166 (mppt) REVERT: J 46 GLU cc_start: 0.8782 (pt0) cc_final: 0.8301 (pm20) REVERT: J 64 VAL cc_start: 0.9149 (m) cc_final: 0.8532 (t) REVERT: J 101 LEU cc_start: 0.9046 (tp) cc_final: 0.8841 (tp) REVERT: J 102 GLN cc_start: 0.8358 (mt0) cc_final: 0.7858 (mt0) REVERT: J 128 THR cc_start: 0.9352 (m) cc_final: 0.9151 (t) REVERT: M 24 ARG cc_start: 0.7417 (mmm-85) cc_final: 0.7073 (mmm-85) REVERT: M 55 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7161 (tm-30) REVERT: M 73 LEU cc_start: 0.7987 (tp) cc_final: 0.7508 (tp) REVERT: M 90 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7242 (tp40) REVERT: F 581 THR cc_start: 0.9648 (m) cc_final: 0.9362 (p) REVERT: F 592 PHE cc_start: 0.8244 (t80) cc_final: 0.7796 (t80) REVERT: S 4 LEU cc_start: 0.8419 (mt) cc_final: 0.8176 (mt) REVERT: P 15 SER cc_start: 0.8882 (m) cc_final: 0.8161 (p) REVERT: P 32 TYR cc_start: 0.8762 (m-10) cc_final: 0.8476 (m-10) REVERT: P 60 ASN cc_start: 0.9257 (t0) cc_final: 0.8876 (t0) REVERT: P 111 MET cc_start: 0.8357 (mtm) cc_final: 0.8039 (mtt) outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 0.1510 time to fit residues: 133.1609 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 : 0.738 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN N 77 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN ** 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.101825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.071444 restraints weight = 55343.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.073648 restraints weight = 31140.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.075045 restraints weight = 22013.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075879 restraints weight = 17952.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.076356 restraints weight = 15922.087| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 19314 Z= 0.343 Angle : 0.850 12.369 26295 Z= 0.424 Chirality : 0.052 0.363 2952 Planarity : 0.005 0.069 3315 Dihedral : 7.729 40.559 3141 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -1.36 (0.17), residues: 2340 helix: 0.32 (0.38), residues: 183 sheet: -0.87 (0.17), residues: 903 loop : -1.04 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 18 TYR 0.034 0.003 TYR I 114 PHE 0.021 0.003 PHE D 582 TRP 0.021 0.003 TRP O 114 HIS 0.013 0.002 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00778 (19266) covalent geometry : angle 0.82160 (26172) SS BOND : bond 0.00712 ( 21) SS BOND : angle 1.92987 ( 42) hydrogen bonds : bond 0.04102 ( 622) hydrogen bonds : angle 6.31220 ( 1749) link_ALPHA1-3 : bond 0.01113 ( 3) link_ALPHA1-3 : angle 2.14670 ( 9) link_ALPHA1-6 : bond 0.00194 ( 3) link_ALPHA1-6 : angle 2.22761 ( 9) link_BETA1-4 : bond 0.00647 ( 6) link_BETA1-4 : angle 2.92253 ( 18) link_NAG-ASN : bond 0.00398 ( 15) link_NAG-ASN : angle 4.52612 ( 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 521 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 0.762 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 39 HIS cc_start: 0.8343 (t70) cc_final: 0.8136 (t-170) REVERT: A 56 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7058 (mmmt) REVERT: A 62 GLN cc_start: 0.9329 (mt0) cc_final: 0.8664 (mt0) REVERT: A 78 ASP cc_start: 0.8362 (t0) cc_final: 0.8119 (t0) REVERT: A 103 GLU cc_start: 0.8396 (tt0) cc_final: 0.8172 (tt0) REVERT: A 117 ASP cc_start: 0.8582 (p0) cc_final: 0.8261 (p0) REVERT: H 48 MET cc_start: 0.8458 (mmm) cc_final: 0.8210 (mmp) REVERT: H 114 TYR cc_start: 0.6282 (m-10) cc_final: 0.5792 (m-10) REVERT: H 115 TYR cc_start: 0.8859 (m-10) cc_final: 0.8584 (m-10) REVERT: K 81 GLU cc_start: 0.8621 (mp0) cc_final: 0.8405 (mp0) REVERT: D 512 ASN cc_start: 0.9123 (t0) cc_final: 0.8835 (t0) REVERT: D 564 GLU cc_start: 0.7977 (mp0) cc_final: 0.7680 (mp0) REVERT: D 565 THR cc_start: 0.9280 (p) cc_final: 0.8968 (t) REVERT: Q 61 ASP cc_start: 0.8264 (p0) cc_final: 0.7954 (p0) REVERT: N 15 SER cc_start: 0.8615 (m) cc_final: 0.8248 (p) REVERT: B 47 ASP cc_start: 0.6460 (t0) cc_final: 0.6120 (t0) REVERT: B 56 LYS cc_start: 0.7785 (mmpt) cc_final: 0.7562 (mmmt) REVERT: B 62 GLN cc_start: 0.9066 (mt0) cc_final: 0.8554 (mt0) REVERT: B 272 LYS cc_start: 0.4894 (pttt) cc_final: 0.4098 (ttmm) REVERT: I 46 GLU cc_start: 0.8793 (pt0) cc_final: 0.8322 (pm20) REVERT: I 48 MET cc_start: 0.8442 (mmm) cc_final: 0.8208 (tpp) REVERT: I 59 PHE cc_start: 0.7584 (t80) cc_final: 0.6716 (t80) REVERT: I 76 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8365 (ptpp) REVERT: I 80 TYR cc_start: 0.8335 (m-80) cc_final: 0.7152 (m-80) REVERT: L 31 ASN cc_start: 0.7341 (p0) cc_final: 0.6856 (m-40) REVERT: L 73 LEU cc_start: 0.8333 (tp) cc_final: 0.7987 (tp) REVERT: E 532 ILE cc_start: 0.9326 (mt) cc_final: 0.9105 (pt) REVERT: E 555 ILE cc_start: 0.9415 (mt) cc_final: 0.9126 (mt) REVERT: E 565 THR cc_start: 0.9276 (p) cc_final: 0.8921 (t) REVERT: E 581 THR cc_start: 0.9643 (m) cc_final: 0.9326 (p) REVERT: E 597 TRP cc_start: 0.7660 (t-100) cc_final: 0.7060 (t-100) REVERT: R 18 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7721 (ttp80) REVERT: R 61 ASP cc_start: 0.8415 (p0) cc_final: 0.8003 (t0) REVERT: O 16 GLU cc_start: 0.8590 (pt0) cc_final: 0.8177 (pt0) REVERT: C 62 GLN cc_start: 0.9132 (mt0) cc_final: 0.8583 (mt0) REVERT: C 117 ASP cc_start: 0.8729 (p0) cc_final: 0.8417 (p0) REVERT: C 172 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8033 (ttm110) REVERT: J 12 VAL cc_start: 0.6848 (t) cc_final: 0.6542 (t) REVERT: J 31 ASN cc_start: 0.8370 (t0) cc_final: 0.8105 (t0) REVERT: J 35 HIS cc_start: 0.8402 (m-70) cc_final: 0.7981 (m170) REVERT: J 46 GLU cc_start: 0.8870 (pt0) cc_final: 0.8308 (pm20) REVERT: J 59 PHE cc_start: 0.7156 (t80) cc_final: 0.6955 (t80) REVERT: J 86 LEU cc_start: 0.9146 (mt) cc_final: 0.8750 (mt) REVERT: J 101 LEU cc_start: 0.9086 (tp) cc_final: 0.8851 (tp) REVERT: J 102 GLN cc_start: 0.8344 (mt0) cc_final: 0.7928 (mt0) REVERT: M 24 ARG cc_start: 0.7563 (mmm-85) cc_final: 0.7257 (mmm-85) REVERT: M 55 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7343 (tm-30) REVERT: M 69 THR cc_start: 0.8603 (p) cc_final: 0.8399 (p) REVERT: M 73 LEU cc_start: 0.8018 (tp) cc_final: 0.7544 (tp) REVERT: F 578 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8367 (mm-30) REVERT: P 15 SER cc_start: 0.8878 (m) cc_final: 0.8301 (p) REVERT: P 32 TYR cc_start: 0.8902 (m-10) cc_final: 0.8617 (m-10) REVERT: P 60 ASN cc_start: 0.9305 (t0) cc_final: 0.9013 (t0) REVERT: P 111 MET cc_start: 0.8613 (mtm) cc_final: 0.8215 (mtt) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.1444 time to fit residues: 115.1335 Evaluate side-chains 421 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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: 1.9990 chunk 105 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN H 31 ASN ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN N 77 GLN B 255 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 27 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.106039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075616 restraints weight = 54431.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.077988 restraints weight = 30052.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079481 restraints weight = 20995.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.080420 restraints weight = 17009.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.080846 restraints weight = 14982.995| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19314 Z= 0.162 Angle : 0.724 10.567 26295 Z= 0.363 Chirality : 0.049 0.348 2952 Planarity : 0.004 0.055 3315 Dihedral : 6.979 38.914 3141 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -1.01 (0.18), residues: 2340 helix: 0.51 (0.37), residues: 201 sheet: -0.57 (0.17), residues: 873 loop : -0.87 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 61 TYR 0.025 0.002 TYR I 116 PHE 0.032 0.002 PHE Q 34 TRP 0.013 0.001 TRP O 114 HIS 0.012 0.001 HIS I 112 Details of bonding type rmsd covalent geometry : bond 0.00367 (19266) covalent geometry : angle 0.69763 (26172) SS BOND : bond 0.00553 ( 21) SS BOND : angle 1.65509 ( 42) hydrogen bonds : bond 0.03518 ( 622) hydrogen bonds : angle 5.90709 ( 1749) link_ALPHA1-3 : bond 0.01082 ( 3) link_ALPHA1-3 : angle 1.78076 ( 9) link_ALPHA1-6 : bond 0.00438 ( 3) link_ALPHA1-6 : angle 1.86058 ( 9) link_BETA1-4 : bond 0.00463 ( 6) link_BETA1-4 : angle 2.86474 ( 18) link_NAG-ASN : bond 0.00597 ( 15) link_NAG-ASN : angle 4.04793 ( 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 560 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 0.786 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: A 62 GLN cc_start: 0.9180 (mt0) cc_final: 0.8950 (mt0) REVERT: A 78 ASP cc_start: 0.8336 (t0) cc_final: 0.8001 (t0) REVERT: A 117 ASP cc_start: 0.8550 (p0) cc_final: 0.8229 (p0) REVERT: H 114 TYR cc_start: 0.6287 (m-10) cc_final: 0.5634 (m-10) REVERT: H 115 TYR cc_start: 0.8837 (m-10) cc_final: 0.8558 (m-10) REVERT: K 81 GLU cc_start: 0.8638 (mp0) cc_final: 0.8410 (mp0) REVERT: K 104 LEU cc_start: 0.7249 (tp) cc_final: 0.6820 (tp) REVERT: D 512 ASN cc_start: 0.9039 (t0) cc_final: 0.8828 (t0) REVERT: D 560 GLN cc_start: 0.8858 (tp40) cc_final: 0.7437 (tp-100) REVERT: D 564 GLU cc_start: 0.7862 (mp0) cc_final: 0.7415 (mp0) REVERT: D 565 THR cc_start: 0.9208 (p) cc_final: 0.8890 (t) REVERT: D 579 LEU cc_start: 0.9141 (mm) cc_final: 0.8707 (tp) REVERT: D 581 THR cc_start: 0.9627 (m) cc_final: 0.9368 (p) REVERT: Q 61 ASP cc_start: 0.8070 (p0) cc_final: 0.7867 (p0) REVERT: Q 71 ASP cc_start: 0.7589 (t0) cc_final: 0.7384 (t0) REVERT: N 15 SER cc_start: 0.8580 (m) cc_final: 0.8164 (p) REVERT: B 47 ASP cc_start: 0.6543 (t0) cc_final: 0.6041 (t0) REVERT: B 62 GLN cc_start: 0.9119 (mt0) cc_final: 0.8562 (mt0) REVERT: B 117 ASP cc_start: 0.8668 (p0) cc_final: 0.8420 (p0) REVERT: I 46 GLU cc_start: 0.8717 (pt0) cc_final: 0.8234 (pm20) REVERT: I 59 PHE cc_start: 0.7503 (t80) cc_final: 0.6590 (t80) REVERT: I 76 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8404 (ptpp) REVERT: I 80 TYR cc_start: 0.8319 (m-80) cc_final: 0.7255 (m-80) REVERT: I 83 MET cc_start: 0.8521 (mmm) cc_final: 0.7835 (mmp) REVERT: L 31 ASN cc_start: 0.7245 (p0) cc_final: 0.6673 (m-40) REVERT: L 69 THR cc_start: 0.8308 (p) cc_final: 0.8090 (p) REVERT: L 70 ASP cc_start: 0.7171 (t0) cc_final: 0.6724 (p0) REVERT: L 73 LEU cc_start: 0.8412 (tp) cc_final: 0.8035 (tp) REVERT: E 514 ASN cc_start: 0.9178 (m-40) cc_final: 0.8752 (m-40) REVERT: E 555 ILE cc_start: 0.9190 (mt) cc_final: 0.8920 (mt) REVERT: E 560 GLN cc_start: 0.9069 (tp40) cc_final: 0.8019 (tp40) REVERT: E 565 THR cc_start: 0.9139 (p) cc_final: 0.8847 (t) REVERT: E 581 THR cc_start: 0.9625 (m) cc_final: 0.9350 (p) REVERT: R 61 ASP cc_start: 0.8323 (p0) cc_final: 0.7902 (t0) REVERT: C 62 GLN cc_start: 0.9045 (mt0) cc_final: 0.8553 (mt0) REVERT: C 68 LEU cc_start: 0.9390 (mt) cc_final: 0.9085 (mt) REVERT: C 117 ASP cc_start: 0.8659 (p0) cc_final: 0.8340 (p0) REVERT: C 172 ARG cc_start: 0.8652 (ttm110) cc_final: 0.8283 (ttm110) REVERT: J 12 VAL cc_start: 0.6691 (t) cc_final: 0.6343 (t) REVERT: J 46 GLU cc_start: 0.8856 (pt0) cc_final: 0.8301 (pm20) REVERT: J 102 GLN cc_start: 0.8262 (mt0) cc_final: 0.7828 (mt0) REVERT: M 24 ARG cc_start: 0.7525 (mmm-85) cc_final: 0.7217 (mmm-85) REVERT: M 55 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7333 (tm-30) REVERT: M 73 LEU cc_start: 0.8044 (tp) cc_final: 0.7542 (tp) REVERT: P 15 SER cc_start: 0.8840 (m) cc_final: 0.8158 (p) REVERT: P 45 LEU cc_start: 0.8814 (mt) cc_final: 0.8489 (mt) REVERT: P 60 ASN cc_start: 0.9281 (t0) cc_final: 0.8966 (t0) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 0.1491 time to fit residues: 126.6497 Evaluate side-chains 446 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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: 0.0970 chunk 154 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 85 optimal weight: 0.0060 chunk 144 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Q 39 GLN N 76 ASN N 77 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 35 HIS ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078241 restraints weight = 53606.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.080696 restraints weight = 29177.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.082252 restraints weight = 20192.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.083169 restraints weight = 16194.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.083676 restraints weight = 14246.582| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19314 Z= 0.127 Angle : 0.701 10.278 26295 Z= 0.349 Chirality : 0.048 0.321 2952 Planarity : 0.004 0.048 3315 Dihedral : 6.413 38.595 3141 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % 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: -0.78 (0.18), residues: 2340 helix: 0.53 (0.38), residues: 198 sheet: -0.27 (0.18), residues: 834 loop : -0.80 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 38 TYR 0.031 0.002 TYR I 114 PHE 0.051 0.002 PHE Q 34 TRP 0.014 0.001 TRP B 275 HIS 0.009 0.002 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00284 (19266) covalent geometry : angle 0.67832 (26172) SS BOND : bond 0.00440 ( 21) SS BOND : angle 1.20379 ( 42) hydrogen bonds : bond 0.03315 ( 622) hydrogen bonds : angle 5.55950 ( 1749) link_ALPHA1-3 : bond 0.01067 ( 3) link_ALPHA1-3 : angle 1.41040 ( 9) link_ALPHA1-6 : bond 0.00561 ( 3) link_ALPHA1-6 : angle 1.66063 ( 9) link_BETA1-4 : bond 0.00519 ( 6) link_BETA1-4 : angle 2.80232 ( 18) link_NAG-ASN : bond 0.00648 ( 15) link_NAG-ASN : angle 3.73203 ( 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 576 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9205 (mt0) cc_final: 0.8566 (mt0) REVERT: A 78 ASP cc_start: 0.8263 (t0) cc_final: 0.7914 (t0) REVERT: A 117 ASP cc_start: 0.8500 (p0) cc_final: 0.8195 (p0) REVERT: A 253 LEU cc_start: 0.9308 (mp) cc_final: 0.9101 (mp) REVERT: A 272 LYS cc_start: 0.4706 (pttt) cc_final: 0.4431 (pttm) REVERT: H 52 ARG cc_start: 0.8822 (mtm-85) cc_final: 0.8263 (mtt90) REVERT: H 74 ASN cc_start: 0.7907 (m-40) cc_final: 0.7232 (t0) REVERT: H 114 TYR cc_start: 0.6116 (m-10) cc_final: 0.5647 (m-10) REVERT: K 81 GLU cc_start: 0.8720 (mp0) cc_final: 0.8466 (mp0) REVERT: K 106 ILE cc_start: 0.3745 (tp) cc_final: 0.2875 (mm) REVERT: D 560 GLN cc_start: 0.8744 (tp40) cc_final: 0.7800 (tm-30) REVERT: D 565 THR cc_start: 0.9235 (p) cc_final: 0.8898 (t) REVERT: D 579 LEU cc_start: 0.9021 (mm) cc_final: 0.8708 (tp) REVERT: D 581 THR cc_start: 0.9571 (m) cc_final: 0.9324 (p) REVERT: D 592 PHE cc_start: 0.8394 (t80) cc_final: 0.8010 (t80) REVERT: Q 90 GLN cc_start: 0.7849 (tt0) cc_final: 0.7102 (pt0) REVERT: N 15 SER cc_start: 0.8600 (m) cc_final: 0.7424 (p) REVERT: N 39 GLN cc_start: 0.8585 (tt0) cc_final: 0.8322 (tt0) REVERT: B 47 ASP cc_start: 0.6653 (t0) cc_final: 0.6095 (t0) REVERT: B 62 GLN cc_start: 0.9118 (mt0) cc_final: 0.8614 (mt0) REVERT: B 117 ASP cc_start: 0.8644 (p0) cc_final: 0.8402 (p0) REVERT: I 46 GLU cc_start: 0.8669 (pt0) cc_final: 0.8180 (pm20) REVERT: I 59 PHE cc_start: 0.7528 (t80) cc_final: 0.6801 (t80) REVERT: I 80 TYR cc_start: 0.8298 (m-80) cc_final: 0.7383 (m-80) REVERT: I 83 MET cc_start: 0.8528 (mmm) cc_final: 0.7649 (mmp) REVERT: L 31 ASN cc_start: 0.7215 (p0) cc_final: 0.6821 (m-40) REVERT: L 69 THR cc_start: 0.8323 (p) cc_final: 0.8103 (p) REVERT: L 70 ASP cc_start: 0.7219 (t0) cc_final: 0.6782 (p0) REVERT: L 73 LEU cc_start: 0.8370 (tp) cc_final: 0.7960 (tp) REVERT: L 104 LEU cc_start: 0.7676 (tp) cc_final: 0.7389 (tt) REVERT: E 514 ASN cc_start: 0.9024 (m-40) cc_final: 0.8379 (m-40) REVERT: E 555 ILE cc_start: 0.9137 (mt) cc_final: 0.8822 (mt) REVERT: E 560 GLN cc_start: 0.8970 (tp40) cc_final: 0.7869 (tp40) REVERT: E 564 GLU cc_start: 0.7797 (mp0) cc_final: 0.7585 (mp0) REVERT: E 565 THR cc_start: 0.9143 (p) cc_final: 0.8842 (t) REVERT: E 579 LEU cc_start: 0.8952 (mm) cc_final: 0.8732 (tp) REVERT: E 581 THR cc_start: 0.9540 (m) cc_final: 0.9246 (p) REVERT: E 597 TRP cc_start: 0.7302 (t-100) cc_final: 0.6971 (t-100) REVERT: R 18 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7548 (ttp80) REVERT: R 61 ASP cc_start: 0.8219 (p0) cc_final: 0.7836 (t0) REVERT: R 82 GLU cc_start: 0.8219 (pm20) cc_final: 0.7721 (pm20) REVERT: R 96 LEU cc_start: 0.9399 (mt) cc_final: 0.8944 (tt) REVERT: O 16 GLU cc_start: 0.8529 (pt0) cc_final: 0.8214 (pt0) REVERT: C 56 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7561 (mmmt) REVERT: C 62 GLN cc_start: 0.9097 (mt0) cc_final: 0.8546 (mt0) REVERT: C 68 LEU cc_start: 0.9336 (mt) cc_final: 0.9068 (mt) REVERT: C 117 ASP cc_start: 0.8673 (p0) cc_final: 0.8467 (p0) REVERT: C 172 ARG cc_start: 0.8532 (ttm110) cc_final: 0.8094 (ttm110) REVERT: J 12 VAL cc_start: 0.6792 (t) cc_final: 0.6514 (t) REVERT: J 46 GLU cc_start: 0.8806 (pt0) cc_final: 0.8232 (pm20) REVERT: J 86 LEU cc_start: 0.8963 (mt) cc_final: 0.8735 (mt) REVERT: J 101 LEU cc_start: 0.8835 (tp) cc_final: 0.7916 (mt) REVERT: J 102 GLN cc_start: 0.8254 (mt0) cc_final: 0.7145 (mt0) REVERT: J 114 TYR cc_start: 0.6338 (m-10) cc_final: 0.5639 (m-10) REVERT: J 115 TYR cc_start: 0.8918 (m-10) cc_final: 0.8695 (m-10) REVERT: M 24 ARG cc_start: 0.7486 (mmm-85) cc_final: 0.7117 (mmm-85) REVERT: M 55 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7338 (tm-30) REVERT: M 69 THR cc_start: 0.8345 (p) cc_final: 0.8140 (p) REVERT: M 73 LEU cc_start: 0.7988 (tp) cc_final: 0.7489 (tp) REVERT: F 540 GLU cc_start: 0.8635 (mp0) cc_final: 0.8392 (tm-30) REVERT: F 560 GLN cc_start: 0.9100 (tp40) cc_final: 0.8282 (tp40) REVERT: S 4 LEU cc_start: 0.8405 (mt) cc_final: 0.8155 (mt) REVERT: S 96 LEU cc_start: 0.9446 (mp) cc_final: 0.9193 (tt) REVERT: P 15 SER cc_start: 0.8879 (m) cc_final: 0.8034 (p) REVERT: P 20 LEU cc_start: 0.9046 (mp) cc_final: 0.8779 (mp) REVERT: P 45 LEU cc_start: 0.8883 (mt) cc_final: 0.8660 (mt) REVERT: P 60 ASN cc_start: 0.9229 (t0) cc_final: 0.8922 (t0) REVERT: P 112 ASP cc_start: 0.8838 (p0) cc_final: 0.8598 (p0) outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.1445 time to fit residues: 127.0472 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 : 0.769 ------------------------------------------------------------------------------- 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: 8.9990 chunk 3 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 chunk 191 optimal weight: 0.0870 chunk 175 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN N 77 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078272 restraints weight = 54331.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.080655 restraints weight = 29697.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082191 restraints weight = 20697.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.083132 restraints weight = 16694.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083585 restraints weight = 14664.248| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19314 Z= 0.134 Angle : 0.702 10.953 26295 Z= 0.353 Chirality : 0.048 0.312 2952 Planarity : 0.004 0.075 3315 Dihedral : 6.174 37.590 3141 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.80 (0.18), residues: 2340 helix: 0.46 (0.37), residues: 201 sheet: -0.37 (0.17), residues: 921 loop : -0.74 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 172 TYR 0.031 0.002 TYR I 116 PHE 0.048 0.002 PHE Q 34 TRP 0.021 0.001 TRP F 531 HIS 0.014 0.002 HIS O 52 Details of bonding type rmsd covalent geometry : bond 0.00303 (19266) covalent geometry : angle 0.68104 (26172) SS BOND : bond 0.00803 ( 21) SS BOND : angle 1.40458 ( 42) hydrogen bonds : bond 0.03364 ( 622) hydrogen bonds : angle 5.50250 ( 1749) link_ALPHA1-3 : bond 0.01203 ( 3) link_ALPHA1-3 : angle 1.42480 ( 9) link_ALPHA1-6 : bond 0.00526 ( 3) link_ALPHA1-6 : angle 1.58249 ( 9) link_BETA1-4 : bond 0.00548 ( 6) link_BETA1-4 : angle 2.86066 ( 18) link_NAG-ASN : bond 0.00584 ( 15) link_NAG-ASN : angle 3.54498 ( 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 559 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 0.802 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 62 GLN cc_start: 0.9194 (mt0) cc_final: 0.8567 (mt0) REVERT: A 78 ASP cc_start: 0.8236 (t0) cc_final: 0.7920 (t0) REVERT: A 117 ASP cc_start: 0.8530 (p0) cc_final: 0.8235 (p0) REVERT: A 272 LYS cc_start: 0.4733 (pttt) cc_final: 0.4435 (pttm) REVERT: H 52 ARG cc_start: 0.8829 (mtm-85) cc_final: 0.8263 (mtt90) REVERT: H 114 TYR cc_start: 0.6208 (m-10) cc_final: 0.5688 (m-10) REVERT: K 55 GLN cc_start: 0.7542 (tm-30) cc_final: 0.7167 (tm-30) REVERT: D 560 GLN cc_start: 0.8859 (tp40) cc_final: 0.7929 (tm-30) REVERT: D 565 THR cc_start: 0.9276 (p) cc_final: 0.9003 (t) REVERT: D 579 LEU cc_start: 0.9083 (mm) cc_final: 0.8817 (tt) REVERT: D 581 THR cc_start: 0.9619 (m) cc_final: 0.9343 (p) REVERT: D 592 PHE cc_start: 0.8381 (t80) cc_final: 0.8044 (t80) REVERT: Q 33 TYR cc_start: 0.6933 (m-10) cc_final: 0.6590 (m-10) REVERT: Q 90 GLN cc_start: 0.7858 (tt0) cc_final: 0.7196 (pt0) REVERT: N 15 SER cc_start: 0.8575 (m) cc_final: 0.7382 (p) REVERT: B 47 ASP cc_start: 0.6656 (t0) cc_final: 0.6119 (t0) REVERT: B 62 GLN cc_start: 0.9126 (mt0) cc_final: 0.8603 (mt0) REVERT: B 78 ASP cc_start: 0.8082 (t70) cc_final: 0.7842 (p0) REVERT: B 117 ASP cc_start: 0.8623 (p0) cc_final: 0.8381 (p0) REVERT: I 45 LEU cc_start: 0.7612 (tp) cc_final: 0.7370 (tp) REVERT: I 46 GLU cc_start: 0.8766 (pt0) cc_final: 0.8505 (pm20) REVERT: I 59 PHE cc_start: 0.7520 (t80) cc_final: 0.6942 (t80) REVERT: I 80 TYR cc_start: 0.8163 (m-80) cc_final: 0.7911 (m-80) REVERT: L 70 ASP cc_start: 0.7331 (t0) cc_final: 0.6843 (p0) REVERT: L 73 LEU cc_start: 0.8345 (tp) cc_final: 0.7818 (tp) REVERT: E 514 ASN cc_start: 0.8938 (m-40) cc_final: 0.8539 (m-40) REVERT: E 555 ILE cc_start: 0.9049 (mt) cc_final: 0.8750 (mt) REVERT: E 560 GLN cc_start: 0.8973 (tp40) cc_final: 0.7898 (tp40) REVERT: E 564 GLU cc_start: 0.7794 (mp0) cc_final: 0.7439 (mp0) REVERT: E 565 THR cc_start: 0.9180 (p) cc_final: 0.8916 (t) REVERT: E 581 THR cc_start: 0.9571 (m) cc_final: 0.9247 (p) REVERT: R 18 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7514 (ttp80) REVERT: R 61 ASP cc_start: 0.8205 (p0) cc_final: 0.7829 (t0) REVERT: R 96 LEU cc_start: 0.9406 (mt) cc_final: 0.8931 (tt) REVERT: O 15 SER cc_start: 0.8971 (m) cc_final: 0.8620 (p) REVERT: O 16 GLU cc_start: 0.8361 (pt0) cc_final: 0.8003 (pt0) REVERT: C 56 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7466 (mmmt) REVERT: C 62 GLN cc_start: 0.9091 (mt0) cc_final: 0.8557 (mt0) REVERT: C 172 ARG cc_start: 0.8505 (ttm110) cc_final: 0.8065 (ttm110) REVERT: J 12 VAL cc_start: 0.6871 (t) cc_final: 0.6613 (t) REVERT: J 46 GLU cc_start: 0.8796 (pt0) cc_final: 0.8302 (pm20) REVERT: J 48 MET cc_start: 0.8262 (mmm) cc_final: 0.7983 (mmp) REVERT: J 101 LEU cc_start: 0.8797 (tp) cc_final: 0.7808 (mt) REVERT: J 102 GLN cc_start: 0.8240 (mt0) cc_final: 0.7283 (mt0) REVERT: J 114 TYR cc_start: 0.6356 (m-10) cc_final: 0.5622 (m-10) REVERT: J 115 TYR cc_start: 0.8946 (m-10) cc_final: 0.8726 (m-10) REVERT: M 31 ASN cc_start: 0.8229 (t0) cc_final: 0.7952 (t0) REVERT: M 55 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7442 (tm-30) REVERT: M 69 THR cc_start: 0.8229 (p) cc_final: 0.7894 (p) REVERT: M 70 ASP cc_start: 0.7606 (t0) cc_final: 0.6924 (p0) REVERT: M 73 LEU cc_start: 0.7956 (tp) cc_final: 0.7502 (tp) REVERT: M 104 LEU cc_start: 0.7739 (tp) cc_final: 0.7319 (tp) REVERT: F 560 GLN cc_start: 0.8986 (tp40) cc_final: 0.8039 (tp40) REVERT: F 564 GLU cc_start: 0.8116 (mp0) cc_final: 0.7687 (mp0) REVERT: F 565 THR cc_start: 0.9301 (p) cc_final: 0.9016 (t) REVERT: F 581 THR cc_start: 0.9593 (t) cc_final: 0.9350 (p) REVERT: S 4 LEU cc_start: 0.8429 (mt) cc_final: 0.8165 (mt) REVERT: S 13 LEU cc_start: 0.8174 (mm) cc_final: 0.7922 (mm) REVERT: S 96 LEU cc_start: 0.9395 (mp) cc_final: 0.9178 (tt) REVERT: P 1 GLN cc_start: 0.6727 (mm-40) cc_final: 0.6435 (mm-40) REVERT: P 15 SER cc_start: 0.8880 (m) cc_final: 0.7866 (p) REVERT: P 20 LEU cc_start: 0.9103 (mp) cc_final: 0.8804 (mp) REVERT: P 60 ASN cc_start: 0.9262 (t0) cc_final: 0.8887 (t0) REVERT: P 111 MET cc_start: 0.8016 (mtp) cc_final: 0.7690 (mtp) REVERT: P 112 ASP cc_start: 0.8973 (p0) cc_final: 0.8635 (p0) outliers start: 0 outliers final: 0 residues processed: 559 average time/residue: 0.1437 time to fit residues: 123.2143 Evaluate side-chains 459 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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: 10.0000 chunk 120 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 208 optimal weight: 9.9990 chunk 22 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN N 77 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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 = 0.3661 r_free = 0.3661 target = 0.108917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078893 restraints weight = 54196.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.081328 restraints weight = 29458.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.082906 restraints weight = 20332.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.083874 restraints weight = 16330.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.084318 restraints weight = 14286.081| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19314 Z= 0.132 Angle : 0.709 9.450 26295 Z= 0.355 Chirality : 0.048 0.309 2952 Planarity : 0.004 0.072 3315 Dihedral : 6.000 36.906 3141 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 2340 helix: 0.66 (0.38), residues: 180 sheet: -0.30 (0.17), residues: 918 loop : -0.72 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 172 TYR 0.025 0.002 TYR I 116 PHE 0.038 0.001 PHE Q 34 TRP 0.015 0.001 TRP F 531 HIS 0.011 0.001 HIS O 52 Details of bonding type rmsd covalent geometry : bond 0.00302 (19266) covalent geometry : angle 0.68952 (26172) SS BOND : bond 0.00462 ( 21) SS BOND : angle 1.32905 ( 42) hydrogen bonds : bond 0.03292 ( 622) hydrogen bonds : angle 5.44398 ( 1749) link_ALPHA1-3 : bond 0.01157 ( 3) link_ALPHA1-3 : angle 1.29727 ( 9) link_ALPHA1-6 : bond 0.00629 ( 3) link_ALPHA1-6 : angle 1.60002 ( 9) link_BETA1-4 : bond 0.00539 ( 6) link_BETA1-4 : angle 2.75173 ( 18) link_NAG-ASN : bond 0.00598 ( 15) link_NAG-ASN : angle 3.44499 ( 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 550 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 550 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7548 (mmpt) cc_final: 0.7051 (mmmt) REVERT: A 62 GLN cc_start: 0.9196 (mt0) cc_final: 0.8613 (mt0) REVERT: A 78 ASP cc_start: 0.8196 (t0) cc_final: 0.7887 (t0) REVERT: A 117 ASP cc_start: 0.8544 (p0) cc_final: 0.8257 (p0) REVERT: A 272 LYS cc_start: 0.4734 (pttt) cc_final: 0.4443 (pttm) REVERT: H 52 ARG cc_start: 0.8892 (mtm-85) cc_final: 0.8374 (mtt90) REVERT: K 24 ARG cc_start: 0.7443 (mmm-85) cc_final: 0.6828 (mmm-85) REVERT: K 53 ILE cc_start: 0.9178 (mm) cc_final: 0.8875 (mm) REVERT: K 55 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7339 (tm-30) REVERT: K 69 THR cc_start: 0.8189 (p) cc_final: 0.7743 (p) REVERT: D 560 GLN cc_start: 0.8835 (tp40) cc_final: 0.7928 (tm-30) REVERT: D 565 THR cc_start: 0.9293 (p) cc_final: 0.9007 (t) REVERT: D 578 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8113 (mm-30) REVERT: D 579 LEU cc_start: 0.9024 (mm) cc_final: 0.8760 (tp) REVERT: D 592 PHE cc_start: 0.8358 (t80) cc_final: 0.8024 (t80) REVERT: Q 33 TYR cc_start: 0.6936 (m-10) cc_final: 0.6553 (m-10) REVERT: N 15 SER cc_start: 0.8532 (m) cc_final: 0.7333 (p) REVERT: B 47 ASP cc_start: 0.6743 (t0) cc_final: 0.6221 (t0) REVERT: B 62 GLN cc_start: 0.9109 (mt0) cc_final: 0.8563 (mt0) REVERT: B 78 ASP cc_start: 0.8053 (t70) cc_final: 0.7846 (p0) REVERT: B 117 ASP cc_start: 0.8643 (p0) cc_final: 0.8382 (p0) REVERT: I 59 PHE cc_start: 0.7499 (t80) cc_final: 0.6768 (t80) REVERT: I 80 TYR cc_start: 0.8143 (m-80) cc_final: 0.7884 (m-80) REVERT: L 69 THR cc_start: 0.8355 (p) cc_final: 0.7905 (p) REVERT: L 70 ASP cc_start: 0.7230 (t0) cc_final: 0.6706 (p0) REVERT: L 73 LEU cc_start: 0.8321 (tp) cc_final: 0.7808 (tp) REVERT: E 514 ASN cc_start: 0.9006 (m-40) cc_final: 0.8427 (m-40) REVERT: E 555 ILE cc_start: 0.9063 (mt) cc_final: 0.8757 (mt) REVERT: E 560 GLN cc_start: 0.8960 (tp40) cc_final: 0.7777 (tp40) REVERT: E 564 GLU cc_start: 0.7871 (mp0) cc_final: 0.7425 (mp0) REVERT: E 565 THR cc_start: 0.9246 (p) cc_final: 0.8950 (t) REVERT: E 578 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8282 (mm-30) REVERT: E 581 THR cc_start: 0.9575 (m) cc_final: 0.9243 (p) REVERT: R 18 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7543 (ttp80) REVERT: R 61 ASP cc_start: 0.8091 (p0) cc_final: 0.7782 (t0) REVERT: R 96 LEU cc_start: 0.9374 (mt) cc_final: 0.8893 (tt) REVERT: O 13 LYS cc_start: 0.8904 (tmmt) cc_final: 0.8436 (ttpp) REVERT: O 15 SER cc_start: 0.8937 (m) cc_final: 0.8588 (p) REVERT: O 16 GLU cc_start: 0.8318 (pt0) cc_final: 0.7540 (pt0) REVERT: C 56 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7376 (mmmt) REVERT: C 62 GLN cc_start: 0.9036 (mt0) cc_final: 0.8516 (mt0) REVERT: C 103 GLU cc_start: 0.8693 (pp20) cc_final: 0.8173 (pp20) REVERT: C 172 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8057 (ttm110) REVERT: J 12 VAL cc_start: 0.6926 (t) cc_final: 0.6700 (t) REVERT: J 46 GLU cc_start: 0.8811 (pt0) cc_final: 0.8204 (pm20) REVERT: J 101 LEU cc_start: 0.8799 (tp) cc_final: 0.7799 (mt) REVERT: J 102 GLN cc_start: 0.8222 (mt0) cc_final: 0.7299 (mt0) REVERT: J 114 TYR cc_start: 0.6339 (m-10) cc_final: 0.5615 (m-10) REVERT: J 115 TYR cc_start: 0.8937 (m-10) cc_final: 0.8709 (m-10) REVERT: M 24 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.7088 (mmm-85) REVERT: M 31 ASN cc_start: 0.8195 (t0) cc_final: 0.7961 (t0) REVERT: M 55 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7481 (tm-30) REVERT: M 69 THR cc_start: 0.8141 (p) cc_final: 0.7802 (p) REVERT: M 70 ASP cc_start: 0.7618 (t0) cc_final: 0.6904 (p0) REVERT: M 73 LEU cc_start: 0.7949 (tp) cc_final: 0.7487 (tp) REVERT: M 104 LEU cc_start: 0.7711 (tp) cc_final: 0.7339 (tp) REVERT: F 560 GLN cc_start: 0.8884 (tp40) cc_final: 0.7916 (tp40) REVERT: F 564 GLU cc_start: 0.8074 (mp0) cc_final: 0.7485 (mp0) REVERT: F 565 THR cc_start: 0.9314 (p) cc_final: 0.9027 (t) REVERT: F 581 THR cc_start: 0.9621 (t) cc_final: 0.9383 (p) REVERT: S 4 LEU cc_start: 0.8425 (mt) cc_final: 0.8196 (mt) REVERT: S 11 LEU cc_start: 0.7806 (tp) cc_final: 0.7501 (tp) REVERT: S 96 LEU cc_start: 0.9360 (mp) cc_final: 0.9159 (tt) REVERT: P 1 GLN cc_start: 0.6717 (mm-40) cc_final: 0.6433 (mm-40) REVERT: P 15 SER cc_start: 0.8859 (m) cc_final: 0.7823 (p) REVERT: P 20 LEU cc_start: 0.9060 (mp) cc_final: 0.8753 (mp) REVERT: P 52 HIS cc_start: 0.7827 (t70) cc_final: 0.7588 (t-170) REVERT: P 60 ASN cc_start: 0.9234 (t0) cc_final: 0.8866 (t0) outliers start: 0 outliers final: 0 residues processed: 550 average time/residue: 0.1430 time to fit residues: 121.2594 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 : 0.800 ------------------------------------------------------------------------------- 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: 2.9990 chunk 220 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 D 508 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN ** N 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN N 77 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN ** 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** 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** F 521 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.073658 restraints weight = 55284.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.075866 restraints weight = 31189.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.077301 restraints weight = 22106.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078109 restraints weight = 17968.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.078645 restraints weight = 16040.512| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 19314 Z= 0.289 Angle : 0.824 11.056 26295 Z= 0.412 Chirality : 0.051 0.343 2952 Planarity : 0.005 0.062 3315 Dihedral : 6.496 38.867 3141 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.98 (0.18), residues: 2340 helix: 0.45 (0.38), residues: 183 sheet: -0.63 (0.17), residues: 915 loop : -0.75 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 172 TYR 0.032 0.003 TYR I 116 PHE 0.034 0.003 PHE Q 34 TRP 0.025 0.003 TRP N 114 HIS 0.010 0.002 HIS O 52 Details of bonding type rmsd covalent geometry : bond 0.00658 (19266) covalent geometry : angle 0.80182 (26172) SS BOND : bond 0.00680 ( 21) SS BOND : angle 1.85223 ( 42) hydrogen bonds : bond 0.03805 ( 622) hydrogen bonds : angle 5.83331 ( 1749) link_ALPHA1-3 : bond 0.00989 ( 3) link_ALPHA1-3 : angle 1.67327 ( 9) link_ALPHA1-6 : bond 0.00209 ( 3) link_ALPHA1-6 : angle 2.00493 ( 9) link_BETA1-4 : bond 0.00466 ( 6) link_BETA1-4 : angle 2.67282 ( 18) link_NAG-ASN : bond 0.00420 ( 15) link_NAG-ASN : angle 3.97302 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4065.88 seconds wall clock time: 70 minutes 54.13 seconds (4254.13 seconds total)