Starting phenix.real_space_refine on Mon Sep 14 22:56:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ujz_8561/09_2026/5ujz_8561_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ujz_8561/09_2026/5ujz_8561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ujz_8561/09_2026/5ujz_8561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ujz_8561/09_2026/5ujz_8561.map" model { file = "/net/cci-nas-00/data/ceres_data/5ujz_8561/09_2026/5ujz_8561_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ujz_8561/09_2026/5ujz_8561_trim.cif" } resolution = 4.8 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 ------------------------------------------------------------------------------- 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= 0.071 sd= 0.427 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: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 11004 2.51 5 N 2985 2.21 5 O 3483 1.98 5 H 16401 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33948 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "B" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "C" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "D" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "E" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "F" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "G" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "H" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "I" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.94, per 1000 atoms: 0.15 Number of scatterers: 33948 At special positions: 0 Unit cell: (141.04, 129.56, 182.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 3483 8.00 N 2985 7.00 C 11004 6.00 H 16401 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 637 " distance=2.08 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 648 " distance=2.02 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 637 " distance=2.05 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.04 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS D 644 " - pdb=" SG CYS D 648 " distance=2.02 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 637 " distance=1.96 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 278 " distance=2.04 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.04 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS F 644 " - pdb=" SG CYS F 648 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 406 " - " ASN A 129 " " NAG A 407 " - " ASN A 163 " " NAG A 408 " - " ASN A 15 " " NAG A 409 " - " ASN A 27 " " NAG A 410 " - " ASN A 290 " " NAG B 701 " - " ASN B 654 " " NAG C 406 " - " ASN C 129 " " NAG C 407 " - " ASN C 163 " " NAG C 408 " - " ASN C 15 " " NAG C 409 " - " ASN C 27 " " NAG C 410 " - " ASN C 290 " " NAG D 701 " - " ASN D 654 " " NAG E 406 " - " ASN E 129 " " NAG E 407 " - " ASN E 163 " " NAG E 408 " - " ASN E 15 " " NAG E 409 " - " ASN E 27 " " NAG E 410 " - " ASN E 290 " " NAG F 701 " - " ASN F 654 " " NAG J 1 " - " ASN A 91 " " NAG K 1 " - " ASN A 58 " " NAG L 1 " - " ASN C 91 " " NAG M 1 " - " ASN C 58 " " NAG N 1 " - " ASN E 91 " " NAG O 1 " - " ASN E 58 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 883.4 milliseconds 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 45 sheets defined 18.4% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 removed outlier: 3.977A pdb=" N GLY A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.217A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.980A pdb=" N GLN A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 557 Processing helix chain 'B' and resid 574 through 626 removed outlier: 3.765A pdb=" N GLN B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 626 " --> pdb=" O VAL B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 654 Processing helix chain 'B' and resid 662 through 670 Processing helix chain 'C' and resid 60 through 67 removed outlier: 3.977A pdb=" N GLY C 67 " --> pdb=" O GLY C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.216A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.981A pdb=" N GLN C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 557 Processing helix chain 'D' and resid 574 through 626 removed outlier: 3.766A pdb=" N GLN D 625 " --> pdb=" O LYS D 621 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU D 626 " --> pdb=" O VAL D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 654 Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'E' and resid 60 through 67 removed outlier: 3.977A pdb=" N GLY E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 109 Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.216A pdb=" N TRP E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.981A pdb=" N GLN E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 557 Processing helix chain 'F' and resid 574 through 626 removed outlier: 3.765A pdb=" N GLN F 625 " --> pdb=" O LYS F 621 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU F 626 " --> pdb=" O VAL F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 654 Processing helix chain 'F' and resid 662 through 670 Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'H' and resid 80 through 84 Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'I' and resid 80 through 84 Processing helix chain 'I' and resid 211 through 215 Processing sheet with id=AA1, first strand: chain 'B' and resid 531 through 536 removed outlier: 4.062A pdb=" N CYS B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 22 removed outlier: 6.223A pdb=" N THR A 22 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 48 removed outlier: 5.886A pdb=" N LEU A 45 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS A 278 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.768A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 118 removed outlier: 8.620A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 118 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 140 removed outlier: 4.710A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.956A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 531 through 536 removed outlier: 4.062A pdb=" N CYS D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 22 removed outlier: 6.223A pdb=" N THR C 22 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 48 removed outlier: 5.885A pdb=" N LEU C 45 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS C 278 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.767A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 118 removed outlier: 8.620A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 115 through 118 Processing sheet with id=AB9, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.710A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC2, first strand: chain 'C' and resid 287 through 289 removed outlier: 3.956A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 531 through 536 removed outlier: 4.062A pdb=" N CYS F 637 " --> pdb=" O ILE F 633 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 19 through 22 removed outlier: 6.223A pdb=" N THR E 22 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 48 removed outlier: 5.886A pdb=" N LEU E 45 " --> pdb=" O ASP E 276 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS E 278 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.767A pdb=" N LEU E 54 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 115 through 118 removed outlier: 8.620A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 115 through 118 Processing sheet with id=AD1, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.711A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'E' and resid 287 through 289 removed outlier: 3.957A pdb=" N CYS E 282 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.346A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'G' and resid 129 through 132 removed outlier: 6.016A pdb=" N GLY G 141 " --> pdb=" O ASN G 209 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 136 through 137 removed outlier: 5.311A pdb=" N ASP G 158 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET G 159 " --> pdb=" O GLY G 175 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY G 175 " --> pdb=" O MET G 159 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TRP G 161 " --> pdb=" O VAL G 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 173 " --> pdb=" O TRP G 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.346A pdb=" N GLN H 38 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU H 47 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE3, first strand: chain 'H' and resid 129 through 132 removed outlier: 6.015A pdb=" N GLY H 141 " --> pdb=" O ASN H 209 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 136 through 137 removed outlier: 5.312A pdb=" N ASP H 158 " --> pdb=" O GLY H 223 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N MET H 159 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY H 175 " --> pdb=" O MET H 159 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TRP H 161 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL H 173 " --> pdb=" O TRP H 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.346A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AE8, first strand: chain 'I' and resid 129 through 132 removed outlier: 6.015A pdb=" N GLY I 141 " --> pdb=" O ASN I 209 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 136 through 137 removed outlier: 5.312A pdb=" N ASP I 158 " --> pdb=" O GLY I 223 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N MET I 159 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY I 175 " --> pdb=" O MET I 159 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TRP I 161 " --> pdb=" O VAL I 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL I 173 " --> pdb=" O TRP I 161 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 1935 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: 7.49 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 16395 1.02 - 1.22: 19 1.22 - 1.42: 7734 1.42 - 1.62: 10094 1.62 - 1.82: 102 Bond restraints: 34344 Sorted by residual: bond pdb=" CA GLN G 90 " pdb=" CB GLN G 90 " ideal model delta sigma weight residual 1.530 1.490 0.041 1.50e-02 4.44e+03 7.40e+00 bond pdb=" CA GLN H 90 " pdb=" CB GLN H 90 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.50e-02 4.44e+03 7.22e+00 bond pdb=" CA GLN I 90 " pdb=" CB GLN I 90 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.50e-02 4.44e+03 7.19e+00 bond pdb=" CB GLN G 91 " pdb=" CG GLN G 91 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.96e+00 bond pdb=" CB GLN I 91 " pdb=" CG GLN I 91 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.96e+00 ... (remaining 34339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 57632 2.40 - 4.80: 3486 4.80 - 7.20: 388 7.20 - 9.60: 47 9.60 - 11.99: 4 Bond angle restraints: 61557 Sorted by residual: angle pdb=" N GLY H 31 " pdb=" CA GLY H 31 " pdb=" C GLY H 31 " ideal model delta sigma weight residual 115.08 127.07 -11.99 1.19e+00 7.06e-01 1.02e+02 angle pdb=" N GLY I 31 " pdb=" CA GLY I 31 " pdb=" C GLY I 31 " ideal model delta sigma weight residual 115.08 127.04 -11.96 1.19e+00 7.06e-01 1.01e+02 angle pdb=" N GLY G 31 " pdb=" CA GLY G 31 " pdb=" C GLY G 31 " ideal model delta sigma weight residual 115.08 126.97 -11.89 1.19e+00 7.06e-01 9.99e+01 angle pdb=" C GLU H 1 " pdb=" N ILE H 2 " pdb=" CA ILE H 2 " ideal model delta sigma weight residual 120.35 129.12 -8.77 1.39e+00 5.18e-01 3.98e+01 angle pdb=" C GLU G 1 " pdb=" N ILE G 2 " pdb=" CA ILE G 2 " ideal model delta sigma weight residual 120.35 129.11 -8.76 1.39e+00 5.18e-01 3.98e+01 ... (remaining 61552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.37: 15534 19.37 - 38.73: 943 38.73 - 58.10: 269 58.10 - 77.46: 45 77.46 - 96.83: 15 Dihedral angle restraints: 16806 sinusoidal: 9345 harmonic: 7461 Sorted by residual: dihedral pdb=" CA GLY H 223 " pdb=" C GLY H 223 " pdb=" N VAL H 224 " pdb=" CA VAL H 224 " ideal model delta harmonic sigma weight residual -180.00 -147.21 -32.79 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA GLY G 223 " pdb=" C GLY G 223 " pdb=" N VAL G 224 " pdb=" CA VAL G 224 " ideal model delta harmonic sigma weight residual 180.00 -147.26 -32.74 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA GLY I 223 " pdb=" C GLY I 223 " pdb=" N VAL I 224 " pdb=" CA VAL I 224 " ideal model delta harmonic sigma weight residual -180.00 -147.27 -32.73 0 5.00e+00 4.00e-02 4.28e+01 ... (remaining 16803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1990 0.062 - 0.125: 540 0.125 - 0.187: 130 0.187 - 0.249: 22 0.249 - 0.311: 12 Chirality restraints: 2694 Sorted by residual: chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.80e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.38e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.26e+01 ... (remaining 2691 not shown) Planarity restraints: 5244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 550 " -0.135 2.00e-02 2.50e+03 1.42e-01 3.04e+02 pdb=" CG ASN B 550 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 550 " 0.115 2.00e-02 2.50e+03 pdb=" ND2 ASN B 550 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 550 " 0.217 2.00e-02 2.50e+03 pdb="HD22 ASN B 550 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 550 " 0.131 2.00e-02 2.50e+03 1.42e-01 3.03e+02 pdb=" CG ASN D 550 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN D 550 " -0.118 2.00e-02 2.50e+03 pdb=" ND2 ASN D 550 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 550 " -0.209 2.00e-02 2.50e+03 pdb="HD22 ASN D 550 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 248 " -0.114 2.00e-02 2.50e+03 1.33e-01 2.67e+02 pdb=" CG ASN E 248 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN E 248 " 0.126 2.00e-02 2.50e+03 pdb=" ND2 ASN E 248 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN E 248 " 0.199 2.00e-02 2.50e+03 pdb="HD22 ASN E 248 " -0.195 2.00e-02 2.50e+03 ... (remaining 5241 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.32: 8096 2.32 - 2.89: 76978 2.89 - 3.46: 84880 3.46 - 4.03: 117495 4.03 - 4.60: 176327 Nonbonded interactions: 463776 Sorted by model distance: nonbonded pdb=" H ALA C 13 " pdb=" O TRP D 514 " model vdw 1.744 2.450 nonbonded pdb=" H GLY H 140 " pdb=" O LEU H 210 " model vdw 1.746 2.450 nonbonded pdb=" HE2 HIS A 130 " pdb=" O PRO A 162 " model vdw 1.746 2.450 nonbonded pdb=" HE2 HIS C 130 " pdb=" O PRO C 162 " model vdw 1.746 2.450 nonbonded pdb=" HE2 HIS E 130 " pdb=" O PRO E 162 " model vdw 1.746 2.450 ... (remaining 463771 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } Set refine NCS operators NCS operators will be refined. 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: 0.060 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: 0.230 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 28.660 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.010 0.081 17997 Z= 0.446 Angle : 1.302 11.995 24459 Z= 0.756 Chirality : 0.064 0.311 2694 Planarity : 0.009 0.080 3132 Dihedral : 12.099 96.831 7023 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.60 % Favored : 92.27 % Rotamer: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % 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: -3.77 (0.14), residues: 2172 helix: -1.08 (0.23), residues: 336 sheet: -3.00 (0.18), residues: 510 loop : -2.79 (0.14), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG H 222 TYR 0.028 0.005 TYR C 95 PHE 0.048 0.005 PHE A 147 TRP 0.027 0.005 TRP E 153 HIS 0.018 0.004 HIS D 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00981 / 0.44 (17943) covalent geometry : angle 1.27931 / 0.75 (24318) SS BOND : bond 0.01979 / 1.29 ( 21) SS BOND : angle 2.12651 / 1.19 ( 42) hydrogen bonds : bond 0.10044 / 6.60 ( 675) hydrogen bonds : angle 10.75468 / 7.47 ( 1935) link_BETA1-4 : bond 0.01087 / 0.54 ( 9) link_BETA1-4 : angle 3.95737 / 2.40 ( 27) link_NAG-ASN : bond 0.01466 / 0.90 ( 24) link_NAG-ASN : angle 3.81832 / 2.25 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.145 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: A 18 ASP cc_start: 0.9304 (m-30) cc_final: 0.8600 (p0) REVERT: A 40 SER cc_start: 0.8704 (t) cc_final: 0.8387 (p) REVERT: A 88 ASN cc_start: 0.9107 (m-40) cc_final: 0.8706 (t0) REVERT: A 142 ASN cc_start: 0.8817 (m110) cc_final: 0.8317 (m110) REVERT: A 178 VAL cc_start: 0.8810 (t) cc_final: 0.8577 (p) REVERT: A 237 LEU cc_start: 0.9320 (tp) cc_final: 0.8998 (tt) REVERT: A 299 HIS cc_start: 0.7966 (t-90) cc_final: 0.7090 (t70) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.1255 time to fit residues: 15.4978 Evaluate side-chains 66 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.111 Evaluate side-chains 73 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.060 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: B 542 GLN cc_start: 0.8977 (tp40) cc_final: 0.8722 (tm-30) REVERT: B 549 THR cc_start: 0.9055 (m) cc_final: 0.8854 (p) REVERT: B 551 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7718 (mmtm) REVERT: B 574 GLU cc_start: 0.8609 (mt-10) cc_final: 0.7945 (tt0) REVERT: B 575 ARG cc_start: 0.8379 (mmm-85) cc_final: 0.7899 (ptt180) REVERT: B 603 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8650 (tp30) REVERT: B 610 PHE cc_start: 0.8874 (t80) cc_final: 0.8427 (t80) REVERT: B 638 PHE cc_start: 0.7872 (m-80) cc_final: 0.7409 (m-10) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1173 time to fit residues: 9.4335 Evaluate side-chains 44 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.046 Evaluate side-chains 56 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.056 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: G 13 LEU cc_start: 0.6042 (mt) cc_final: 0.5814 (mt) REVERT: G 208 ASN cc_start: 0.7766 (m-40) cc_final: 0.7409 (p0) REVERT: G 235 PHE cc_start: 0.8683 (p90) cc_final: 0.8331 (p90) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1927 time to fit residues: 11.7300 Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.082 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.0980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN G 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086254 restraints weight = 23489.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.090719 restraints weight = 10922.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.093669 restraints weight = 6007.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.095605 restraints weight = 3624.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.096933 restraints weight = 2314.865| |-----------------------------------------------------------------------------| r_work (final): 0.3556 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.137943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.130607 restraints weight = 20794.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.132500 restraints weight = 9603.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.133615 restraints weight = 4982.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.134219 restraints weight = 2890.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.134593 restraints weight = 1883.477| |-----------------------------------------------------------------------------| r_work (final): 0.3769 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.075494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.065706 restraints weight = 28926.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.068734 restraints weight = 14234.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.070772 restraints weight = 8118.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.072061 restraints weight = 5031.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.072946 restraints weight = 3334.087| |-----------------------------------------------------------------------------| r_work (final): 0.3687 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.052661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.051488 restraints weight = 335.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.051859 restraints weight = 92.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.052136 restraints weight = 45.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.052297 restraints weight = 26.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.052296 restraints weight = 17.278| |-----------------------------------------------------------------------------| r_work (final): 0.2616 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.065980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.065930 restraints weight = 244.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.065957 restraints weight = 21.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.065971 restraints weight = 2.839 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.065971 restraints weight = 0.527 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.065971 restraints weight = 0.527 | |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 17997 Z= 0.204 Angle : 0.840 8.532 24459 Z= 0.451 Chirality : 0.047 0.172 2694 Planarity : 0.007 0.081 3132 Dihedral : 10.950 64.049 3075 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.25 (0.15), residues: 2172 helix: -0.07 (0.27), residues: 345 sheet: -2.82 (0.18), residues: 483 loop : -2.59 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 226 TYR 0.043 0.003 TYR G 33 PHE 0.020 0.002 PHE B 640 TRP 0.014 0.002 TRP D 521 HIS 0.004 0.001 HIS F 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (17943) covalent geometry : angle 0.81540 / 0.45 (24318) SS BOND : bond 0.01942 / 1.24 ( 21) SS BOND : angle 1.82302 / 0.99 ( 42) hydrogen bonds : bond 0.05064 / 3.32 ( 675) hydrogen bonds : angle 8.08499 / 5.62 ( 1935) link_BETA1-4 : bond 0.00950 / 0.53 ( 9) link_BETA1-4 : angle 4.24215 / 2.31 ( 27) link_NAG-ASN : bond 0.00450 / 0.25 ( 24) link_NAG-ASN : angle 2.48700 / 1.57 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.141 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: E 18 ASP cc_start: 0.9491 (m-30) cc_final: 0.8801 (p0) REVERT: E 88 ASN cc_start: 0.9202 (m-40) cc_final: 0.8559 (t0) REVERT: E 178 VAL cc_start: 0.8667 (t) cc_final: 0.8463 (p) REVERT: E 244 ILE cc_start: 0.8959 (mt) cc_final: 0.8225 (mp) REVERT: E 245 PHE cc_start: 0.9246 (m-10) cc_final: 0.8819 (m-80) REVERT: E 246 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7913 (mp0) REVERT: E 299 HIS cc_start: 0.7423 (t-90) cc_final: 0.6581 (t70) outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 0.1229 time to fit residues: 10.1857 Evaluate side-chains 60 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.139 Evaluate side-chains 56 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.074 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: F 515 THR cc_start: 0.8895 (p) cc_final: 0.8521 (t) REVERT: F 551 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7612 (mmtm) REVERT: F 575 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7690 (ptt180) REVERT: F 601 LEU cc_start: 0.8229 (tp) cc_final: 0.7970 (tt) REVERT: F 603 GLU cc_start: 0.9559 (mm-30) cc_final: 0.9252 (tp30) REVERT: F 610 PHE cc_start: 0.9264 (t80) cc_final: 0.8706 (t80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1015 time to fit residues: 6.3159 Evaluate side-chains 41 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.049 Evaluate side-chains 39 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.102 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: H 181 ASP cc_start: 0.8775 (m-30) cc_final: 0.8460 (m-30) REVERT: H 235 PHE cc_start: 0.8893 (p90) cc_final: 0.8657 (p90) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1339 time to fit residues: 5.9273 Evaluate side-chains 26 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.069 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 150 optimal weight: 6.9990 chunk 30 optimal weight: 0.3980 chunk 16 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 0.0570 chunk 143 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 176 optimal weight: 0.4980 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 183 HIS ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 635 ASN H 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.106806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091742 restraints weight = 25720.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.096215 restraints weight = 12789.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.099273 restraints weight = 7357.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.101345 restraints weight = 4613.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102774 restraints weight = 3052.358| |-----------------------------------------------------------------------------| r_work (final): 0.3659 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.136082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.129421 restraints weight = 20672.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.131239 restraints weight = 9650.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.132429 restraints weight = 5240.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.132997 restraints weight = 2966.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.133392 restraints weight = 1971.464| |-----------------------------------------------------------------------------| r_work (final): 0.3876 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.075576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.065723 restraints weight = 29265.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.068910 restraints weight = 14414.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.070933 restraints weight = 8157.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.072274 restraints weight = 5032.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.073110 restraints weight = 3266.518| |-----------------------------------------------------------------------------| r_work (final): 0.3687 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.061297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.059956 restraints weight = 347.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.060597 restraints weight = 98.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.060957 restraints weight = 43.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.061121 restraints weight = 20.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.061219 restraints weight = 10.365| |-----------------------------------------------------------------------------| r_work (final): 0.2812 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.071399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.071359 restraints weight = 163.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.071373 restraints weight = 14.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.071388 restraints weight = 2.031 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.071392 restraints weight = 0.303 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.071392 restraints weight = 0.043 | |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 17997 Z= 0.184 Angle : 0.765 13.192 24459 Z= 0.411 Chirality : 0.046 0.201 2694 Planarity : 0.006 0.048 3132 Dihedral : 9.013 55.767 3075 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.11 (0.15), residues: 2172 helix: 0.08 (0.27), residues: 345 sheet: -2.49 (0.19), residues: 534 loop : -2.58 (0.14), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 322 TYR 0.028 0.002 TYR H 33 PHE 0.015 0.002 PHE B 640 TRP 0.007 0.001 TRP G 36 HIS 0.004 0.001 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (17943) covalent geometry : angle 0.74473 / 0.41 (24318) SS BOND : bond 0.03252 / 1.93 ( 21) SS BOND : angle 2.54514 / 1.40 ( 42) hydrogen bonds : bond 0.04962 / 3.18 ( 675) hydrogen bonds : angle 7.46577 / 5.21 ( 1935) link_BETA1-4 : bond 0.00754 / 0.39 ( 9) link_BETA1-4 : angle 2.82671 / 1.53 ( 27) link_NAG-ASN : bond 0.00397 / 0.22 ( 24) link_NAG-ASN : angle 2.11847 / 1.33 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.105 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: A 18 ASP cc_start: 0.9467 (m-30) cc_final: 0.8561 (p0) REVERT: A 88 ASN cc_start: 0.9263 (m-40) cc_final: 0.8917 (t0) REVERT: A 103 GLU cc_start: 0.8909 (mp0) cc_final: 0.8313 (tt0) REVERT: A 119 GLU cc_start: 0.8978 (pt0) cc_final: 0.8651 (pp20) REVERT: A 178 VAL cc_start: 0.8683 (t) cc_final: 0.8340 (p) REVERT: A 244 ILE cc_start: 0.9083 (mt) cc_final: 0.8134 (mt) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.1032 time to fit residues: 9.1736 Evaluate side-chains 58 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.096 Evaluate side-chains 51 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.073 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: F 503 PHE cc_start: 0.8769 (m-80) cc_final: 0.8535 (m-80) REVERT: F 515 THR cc_start: 0.8829 (p) cc_final: 0.8459 (t) REVERT: F 551 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7479 (mmtt) REVERT: F 575 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7714 (ptt180) REVERT: F 588 PHE cc_start: 0.8866 (m-10) cc_final: 0.8612 (m-80) REVERT: F 603 GLU cc_start: 0.9517 (mm-30) cc_final: 0.9161 (tp30) REVERT: F 610 PHE cc_start: 0.9174 (t80) cc_final: 0.8652 (t80) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1191 time to fit residues: 6.8056 Evaluate side-chains 40 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.073 Evaluate side-chains 36 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.059 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: H 91 GLN cc_start: 0.8440 (tt0) cc_final: 0.8181 (tt0) REVERT: H 181 ASP cc_start: 0.9023 (m-30) cc_final: 0.8549 (m-30) REVERT: H 235 PHE cc_start: 0.8898 (p90) cc_final: 0.8631 (p90) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1065 time to fit residues: 4.4011 Evaluate side-chains 25 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.094 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 142 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 125 optimal weight: 0.0770 chunk 24 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS A 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.102045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086987 restraints weight = 24022.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.091624 restraints weight = 11507.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.094737 restraints weight = 6483.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.096731 restraints weight = 3973.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.098159 restraints weight = 2580.725| |-----------------------------------------------------------------------------| r_work (final): 0.3572 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.136577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.130262 restraints weight = 21414.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.132039 restraints weight = 9628.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.133012 restraints weight = 4859.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.133583 restraints weight = 2789.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.133732 restraints weight = 1820.615| |-----------------------------------------------------------------------------| r_work (final): 0.3877 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.076240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.067099 restraints weight = 29847.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.069966 restraints weight = 14323.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.071855 restraints weight = 8043.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.073088 restraints weight = 4968.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.073921 restraints weight = 3280.287| |-----------------------------------------------------------------------------| r_work (final): 0.3683 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.076163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.071333 restraints weight = 178.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.072916 restraints weight = 94.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.074153 restraints weight = 64.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.075026 restraints weight = 41.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075562 restraints weight = 25.882| |-----------------------------------------------------------------------------| r_work (final): 0.3024 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.072109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.072100 restraints weight = 220.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.072083 restraints weight = 4.401 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.072083 restraints weight = 0.995 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.072083 restraints weight = 0.995 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.072083 restraints weight = 0.995 | |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 17997 Z= 0.152 Angle : 0.703 10.544 24459 Z= 0.375 Chirality : 0.045 0.171 2694 Planarity : 0.005 0.042 3132 Dihedral : 7.625 46.517 3075 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.32 % Allowed : 1.46 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.75 (0.16), residues: 2172 helix: 0.57 (0.27), residues: 342 sheet: -2.31 (0.20), residues: 489 loop : -2.40 (0.14), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 196 TYR 0.027 0.002 TYR H 33 PHE 0.019 0.002 PHE I 154 TRP 0.026 0.002 TRP I 242 HIS 0.005 0.001 HIS D 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (17943) covalent geometry : angle 0.68400 / 0.37 (24318) SS BOND : bond 0.02286 / 1.17 ( 21) SS BOND : angle 2.79557 / 1.63 ( 42) hydrogen bonds : bond 0.04686 / 3.00 ( 675) hydrogen bonds : angle 6.92442 / 4.85 ( 1935) link_BETA1-4 : bond 0.00734 / 0.39 ( 9) link_BETA1-4 : angle 2.12296 / 1.18 ( 27) link_NAG-ASN : bond 0.00345 / 0.20 ( 24) link_NAG-ASN : angle 1.86943 / 1.18 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.098 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: E 18 ASP cc_start: 0.9674 (m-30) cc_final: 0.9261 (p0) REVERT: E 88 ASN cc_start: 0.9420 (m-40) cc_final: 0.8936 (t0) REVERT: E 119 GLU cc_start: 0.9133 (pt0) cc_final: 0.8759 (pp20) REVERT: E 178 VAL cc_start: 0.8988 (t) cc_final: 0.8761 (p) REVERT: E 212 LYS cc_start: 0.9345 (mppt) cc_final: 0.9123 (mmtm) REVERT: E 276 ASP cc_start: 0.5920 (t70) cc_final: 0.5714 (t0) outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 0.0873 time to fit residues: 7.5000 Evaluate side-chains 58 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.135 Evaluate side-chains 49 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.075 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: F 515 THR cc_start: 0.8903 (p) cc_final: 0.8507 (t) REVERT: F 551 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7509 (mmtt) REVERT: F 575 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.7711 (ptt180) REVERT: F 588 PHE cc_start: 0.8883 (m-10) cc_final: 0.8542 (m-80) REVERT: F 591 ILE cc_start: 0.8696 (mm) cc_final: 0.8206 (tt) REVERT: F 603 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9144 (tp30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1131 time to fit residues: 6.1956 Evaluate side-chains 43 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.076 Evaluate side-chains 33 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.093 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: H 181 ASP cc_start: 0.8980 (m-30) cc_final: 0.8504 (m-30) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1318 time to fit residues: 5.0115 Evaluate side-chains 26 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.060 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0008 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 156 optimal weight: 7.9990 chunk 25 optimal weight: 0.0170 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 193 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 183 HIS E 191 GLN E 250 ASN ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.099744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085155 restraints weight = 22483.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.089499 restraints weight = 10689.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.092447 restraints weight = 5990.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.094456 restraints weight = 3677.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.095850 restraints weight = 2399.066| |-----------------------------------------------------------------------------| r_work (final): 0.3543 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.137503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.131148 restraints weight = 21133.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.132930 restraints weight = 9546.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.133945 restraints weight = 4892.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.134504 restraints weight = 2798.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.134815 restraints weight = 1787.979| |-----------------------------------------------------------------------------| r_work (final): 0.3887 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.074355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.064444 restraints weight = 29177.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.067501 restraints weight = 14118.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.069574 restraints weight = 8015.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.070871 restraints weight = 4987.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.071734 restraints weight = 3325.497| |-----------------------------------------------------------------------------| r_work (final): 0.3588 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.076834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.073095 restraints weight = 239.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.074949 restraints weight = 64.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.075816 restraints weight = 36.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.076202 restraints weight = 21.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.076371 restraints weight = 14.099| |-----------------------------------------------------------------------------| r_work (final): 0.3009 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.090752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.086031 restraints weight = 150.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.086709 restraints weight = 90.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.087129 restraints weight = 54.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.087308 restraints weight = 33.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.087428 restraints weight = 23.382| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17997 Z= 0.146 Angle : 0.652 8.593 24459 Z= 0.350 Chirality : 0.042 0.156 2694 Planarity : 0.005 0.043 3132 Dihedral : 7.133 37.647 3075 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.48 (0.16), residues: 2172 helix: 1.04 (0.26), residues: 342 sheet: -2.23 (0.20), residues: 486 loop : -2.24 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 576 TYR 0.026 0.002 TYR H 33 PHE 0.017 0.002 PHE G 100 TRP 0.007 0.001 TRP H 161 HIS 0.003 0.001 HIS E 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (17943) covalent geometry : angle 0.63621 / 0.35 (24318) SS BOND : bond 0.02061 / 1.03 ( 21) SS BOND : angle 1.99052 / 1.12 ( 42) hydrogen bonds : bond 0.04540 / 2.96 ( 675) hydrogen bonds : angle 6.56045 / 4.58 ( 1935) link_BETA1-4 : bond 0.00387 / 0.22 ( 9) link_BETA1-4 : angle 2.18908 / 1.21 ( 27) link_NAG-ASN : bond 0.00346 / 0.19 ( 24) link_NAG-ASN : angle 1.93535 / 1.20 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.134 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: E 18 ASP cc_start: 0.9637 (m-30) cc_final: 0.9285 (p0) REVERT: E 88 ASN cc_start: 0.9418 (m-40) cc_final: 0.8937 (t0) REVERT: E 187 ASN cc_start: 0.9389 (t0) cc_final: 0.9124 (t0) REVERT: E 244 ILE cc_start: 0.8006 (mt) cc_final: 0.7112 (mp) REVERT: E 245 PHE cc_start: 0.9074 (m-10) cc_final: 0.8659 (m-80) outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.0872 time to fit residues: 7.0691 Evaluate side-chains 57 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.134 Evaluate side-chains 52 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.077 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: F 515 THR cc_start: 0.8945 (p) cc_final: 0.8545 (t) REVERT: F 551 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7484 (mmtt) REVERT: F 575 ARG cc_start: 0.8420 (mmm-85) cc_final: 0.7765 (ptt180) REVERT: F 578 GLU cc_start: 0.8611 (tt0) cc_final: 0.8396 (mm-30) REVERT: F 588 PHE cc_start: 0.8920 (m-10) cc_final: 0.8563 (m-80) REVERT: F 590 ASP cc_start: 0.9020 (m-30) cc_final: 0.8819 (m-30) REVERT: F 591 ILE cc_start: 0.8704 (mm) cc_final: 0.8108 (tt) REVERT: F 603 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9191 (tp30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1455 time to fit residues: 8.2165 Evaluate side-chains 44 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.065 Evaluate side-chains 32 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.066 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: I 171 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6603 (mm-30) REVERT: I 207 MET cc_start: 0.8234 (mpp) cc_final: 0.7935 (mpp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1343 time to fit residues: 4.9003 Evaluate side-chains 28 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.086 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 40 optimal weight: 0.9980 chunk 174 optimal weight: 0.0040 chunk 171 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 86 optimal weight: 0.0010 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085616 restraints weight = 24300.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090029 restraints weight = 11608.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.093022 restraints weight = 6516.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.095028 restraints weight = 4002.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.096421 restraints weight = 2591.830| |-----------------------------------------------------------------------------| r_work (final): 0.3536 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.137206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.130782 restraints weight = 20989.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.132631 restraints weight = 10050.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.133673 restraints weight = 5320.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.134224 restraints weight = 3098.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.134593 restraints weight = 2101.037| |-----------------------------------------------------------------------------| r_work (final): 0.3872 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.075909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.067165 restraints weight = 29703.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.069948 restraints weight = 15158.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.071726 restraints weight = 8740.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.072887 restraints weight = 5465.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.073698 restraints weight = 3625.601| |-----------------------------------------------------------------------------| r_work (final): 0.3679 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.070979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.068220 restraints weight = 286.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.069277 restraints weight = 138.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.069690 restraints weight = 80.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.070130 restraints weight = 51.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.070386 restraints weight = 34.101| |-----------------------------------------------------------------------------| r_work (final): 0.2881 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.088309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 12)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083762 restraints weight = 144.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.084273 restraints weight = 83.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.084614 restraints weight = 50.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.084793 restraints weight = 29.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.084862 restraints weight = 18.425| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17997 Z= 0.139 Angle : 0.649 8.146 24459 Z= 0.349 Chirality : 0.042 0.153 2694 Planarity : 0.010 0.270 3132 Dihedral : 6.753 37.056 3075 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.16 % Allowed : 0.65 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.44 (0.16), residues: 2172 helix: 1.20 (0.27), residues: 342 sheet: -2.24 (0.19), residues: 534 loop : -2.22 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 606 TYR 0.025 0.002 TYR G 33 PHE 0.012 0.001 PHE B 570 TRP 0.007 0.001 TRP H 36 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (17943) covalent geometry : angle 0.63347 / 0.34 (24318) SS BOND : bond 0.02031 / 1.03 ( 21) SS BOND : angle 2.29149 / 1.32 ( 42) hydrogen bonds : bond 0.04337 / 2.85 ( 675) hydrogen bonds : angle 6.35526 / 4.44 ( 1935) link_BETA1-4 : bond 0.00613 / 0.33 ( 9) link_BETA1-4 : angle 1.79270 / 0.99 ( 27) link_NAG-ASN : bond 0.00331 / 0.18 ( 24) link_NAG-ASN : angle 1.82201 / 1.13 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.099 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: E 18 ASP cc_start: 0.9612 (m-30) cc_final: 0.9172 (p0) REVERT: E 88 ASN cc_start: 0.9403 (m-40) cc_final: 0.8923 (t0) REVERT: E 180 TRP cc_start: 0.8417 (p90) cc_final: 0.8139 (p90) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.0841 time to fit residues: 6.9916 Evaluate side-chains 53 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.189 Evaluate side-chains 49 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.050 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: F 551 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7488 (mmtt) REVERT: F 575 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7492 (ptt180) REVERT: F 578 GLU cc_start: 0.8653 (tt0) cc_final: 0.8370 (tt0) REVERT: F 588 PHE cc_start: 0.8916 (m-10) cc_final: 0.8536 (m-80) REVERT: F 591 ILE cc_start: 0.8576 (mm) cc_final: 0.8096 (tt) REVERT: F 601 LEU cc_start: 0.8067 (tp) cc_final: 0.7685 (mt) REVERT: F 603 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9158 (tp30) REVERT: F 616 LYS cc_start: 0.9560 (ttmt) cc_final: 0.9346 (ttmm) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1130 time to fit residues: 6.1474 Evaluate side-chains 44 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.075 Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.094 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: H 35 THR cc_start: 0.8457 (m) cc_final: 0.7907 (p) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1313 time to fit residues: 4.5325 Evaluate side-chains 25 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.068 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 46 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 153 optimal weight: 0.3980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.098547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083670 restraints weight = 24271.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088088 restraints weight = 11766.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.091092 restraints weight = 6655.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.093100 restraints weight = 4098.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094527 restraints weight = 2681.922| |-----------------------------------------------------------------------------| r_work (final): 0.3522 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.136820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.130659 restraints weight = 20747.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.132415 restraints weight = 9591.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.133419 restraints weight = 4953.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.133991 restraints weight = 2810.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.134173 restraints weight = 1757.351| |-----------------------------------------------------------------------------| r_work (final): 0.3779 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.074810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.065766 restraints weight = 30658.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.068574 restraints weight = 14625.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.070338 restraints weight = 8309.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.071488 restraints weight = 5256.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.072355 restraints weight = 3581.815| |-----------------------------------------------------------------------------| r_work (final): 0.3634 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.071936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.068700 restraints weight = 332.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.069995 restraints weight = 180.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.070915 restraints weight = 111.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.071477 restraints weight = 64.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.071714 restraints weight = 31.013| |-----------------------------------------------------------------------------| r_work (final): 0.3047 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.087705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.083112 restraints weight = 191.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.083895 restraints weight = 119.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.084300 restraints weight = 80.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.084624 restraints weight = 61.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.084901 restraints weight = 44.812| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17997 Z= 0.179 Angle : 0.639 7.662 24459 Z= 0.346 Chirality : 0.042 0.150 2694 Planarity : 0.006 0.084 3132 Dihedral : 6.385 37.114 3075 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.16 % Allowed : 0.49 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.33 (0.17), residues: 2172 helix: 1.21 (0.27), residues: 342 sheet: -2.06 (0.20), residues: 519 loop : -2.18 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 606 TYR 0.022 0.002 TYR I 33 PHE 0.012 0.002 PHE G 100 TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS E 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (17943) covalent geometry : angle 0.62491 / 0.34 (24318) SS BOND : bond 0.01984 / 1.00 ( 21) SS BOND : angle 2.00173 / 1.12 ( 42) hydrogen bonds : bond 0.04410 / 2.93 ( 675) hydrogen bonds : angle 6.31343 / 4.42 ( 1935) link_BETA1-4 : bond 0.00316 / 0.17 ( 9) link_BETA1-4 : angle 1.73072 / 0.98 ( 27) link_NAG-ASN : bond 0.00381 / 0.20 ( 24) link_NAG-ASN : angle 1.81328 / 1.14 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.143 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: E 18 ASP cc_start: 0.9481 (m-30) cc_final: 0.8846 (p0) REVERT: E 88 ASN cc_start: 0.9454 (m-40) cc_final: 0.8914 (t0) REVERT: E 187 ASN cc_start: 0.9501 (t0) cc_final: 0.9285 (t0) REVERT: E 244 ILE cc_start: 0.7983 (mt) cc_final: 0.7258 (mp) REVERT: E 245 PHE cc_start: 0.9319 (m-80) cc_final: 0.8998 (m-80) outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.0833 time to fit residues: 6.8555 Evaluate side-chains 52 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.145 Evaluate side-chains 46 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.074 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: F 551 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7489 (mmtt) REVERT: F 575 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.7449 (ptt180) REVERT: F 578 GLU cc_start: 0.8813 (tt0) cc_final: 0.8457 (tt0) REVERT: F 591 ILE cc_start: 0.8631 (mm) cc_final: 0.8204 (tt) REVERT: F 601 LEU cc_start: 0.8092 (tp) cc_final: 0.7650 (mt) REVERT: F 603 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9037 (tp30) REVERT: F 616 LYS cc_start: 0.9592 (ttmt) cc_final: 0.9355 (ttmm) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1309 time to fit residues: 6.6834 Evaluate side-chains 42 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.085 Evaluate side-chains 32 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.115 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: H 152 PHE cc_start: 0.7570 (p90) cc_final: 0.7343 (p90) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1466 time to fit residues: 5.3589 Evaluate side-chains 23 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.102 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0007 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 63 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 120 optimal weight: 0.0060 chunk 7 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 199 optimal weight: 0.2980 chunk 214 optimal weight: 0.3980 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086676 restraints weight = 24363.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.090945 restraints weight = 11893.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093832 restraints weight = 6746.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.095755 restraints weight = 4160.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097116 restraints weight = 2736.349| |-----------------------------------------------------------------------------| r_work (final): 0.3553 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.140032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.133529 restraints weight = 20614.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.135471 restraints weight = 9529.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.136467 restraints weight = 4859.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.136989 restraints weight = 2746.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.137320 restraints weight = 1792.211| |-----------------------------------------------------------------------------| r_work (final): 0.3795 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.073637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.064655 restraints weight = 28216.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.067483 restraints weight = 14174.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.069303 restraints weight = 8178.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.070426 restraints weight = 5117.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.071218 restraints weight = 3490.231| |-----------------------------------------------------------------------------| r_work (final): 0.3581 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.073357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.067953 restraints weight = 269.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.069825 restraints weight = 101.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.071090 restraints weight = 65.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.071766 restraints weight = 44.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.072175 restraints weight = 30.454| |-----------------------------------------------------------------------------| r_work (final): 0.2952 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.086814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 18)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.083047 restraints weight = 186.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.083955 restraints weight = 89.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.084489 restraints weight = 47.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.084767 restraints weight = 24.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.084910 restraints weight = 13.085| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 17997 Z= 0.141 Angle : 0.623 7.603 24459 Z= 0.334 Chirality : 0.042 0.153 2694 Planarity : 0.005 0.071 3132 Dihedral : 6.125 36.258 3075 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.16 % Allowed : 0.32 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.27 (0.17), residues: 2172 helix: 1.25 (0.27), residues: 342 sheet: -2.07 (0.20), residues: 534 loop : -2.10 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 229 TYR 0.022 0.002 TYR G 33 PHE 0.011 0.001 PHE B 610 TRP 0.008 0.001 TRP H 242 HIS 0.007 0.001 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (17943) covalent geometry : angle 0.61104 / 0.33 (24318) SS BOND : bond 0.01934 / 0.97 ( 21) SS BOND : angle 1.95283 / 1.11 ( 42) hydrogen bonds : bond 0.04132 / 2.73 ( 675) hydrogen bonds : angle 6.08764 / 4.26 ( 1935) link_BETA1-4 : bond 0.00388 / 0.21 ( 9) link_BETA1-4 : angle 1.57616 / 0.89 ( 27) link_NAG-ASN : bond 0.00305 / 0.16 ( 24) link_NAG-ASN : angle 1.63650 / 1.02 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.114 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: E 18 ASP cc_start: 0.9578 (m-30) cc_final: 0.9174 (p0) REVERT: E 88 ASN cc_start: 0.9391 (m-40) cc_final: 0.8909 (t0) REVERT: E 103 GLU cc_start: 0.8413 (mp0) cc_final: 0.7933 (pt0) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.0711 time to fit residues: 5.7504 Evaluate side-chains 54 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.144 Evaluate side-chains 47 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.071 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: F 575 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.7594 (ptt180) REVERT: F 578 GLU cc_start: 0.8480 (tt0) cc_final: 0.8121 (tt0) REVERT: F 591 ILE cc_start: 0.8120 (mm) cc_final: 0.7688 (tt) REVERT: F 616 LYS cc_start: 0.9506 (ttmt) cc_final: 0.9227 (ttmm) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1343 time to fit residues: 6.9461 Evaluate side-chains 39 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.052 Evaluate side-chains 32 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.093 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: I 152 PHE cc_start: 0.7089 (p90) cc_final: 0.6865 (p90) REVERT: I 171 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7061 (mm-30) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1488 time to fit residues: 5.4389 Evaluate side-chains 24 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.092 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 153 optimal weight: 0.0570 chunk 192 optimal weight: 1.9990 chunk 75 optimal weight: 0.0270 chunk 93 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 185 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 231 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.103856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088678 restraints weight = 23358.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093276 restraints weight = 11053.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.096567 restraints weight = 6154.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.098703 restraints weight = 3692.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.100152 restraints weight = 2350.978| |-----------------------------------------------------------------------------| r_work (final): 0.3643 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.140642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.134252 restraints weight = 20960.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.136108 restraints weight = 9703.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.137122 restraints weight = 4983.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.137692 restraints weight = 2804.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.138018 restraints weight = 1746.174| |-----------------------------------------------------------------------------| r_work (final): 0.3781 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.075393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.066101 restraints weight = 30202.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.069037 restraints weight = 14358.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.070858 restraints weight = 8143.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.072052 restraints weight = 5115.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.072729 restraints weight = 3461.528| |-----------------------------------------------------------------------------| r_work (final): 0.3647 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.073586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.068461 restraints weight = 253.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.070389 restraints weight = 95.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.071428 restraints weight = 59.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.072027 restraints weight = 40.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.072448 restraints weight = 28.573| |-----------------------------------------------------------------------------| r_work (final): 0.2961 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.083546 restraints weight = 166.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.084369 restraints weight = 72.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.084680 restraints weight = 30.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.084773 restraints weight = 8.401 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.084774 restraints weight = 2.910 | |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.6548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 17997 Z= 0.130 Angle : 0.634 8.945 24459 Z= 0.336 Chirality : 0.046 0.386 2694 Planarity : 0.005 0.055 3132 Dihedral : 5.992 34.460 3075 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.13 (0.17), residues: 2172 helix: 1.33 (0.27), residues: 342 sheet: -1.93 (0.20), residues: 534 loop : -2.03 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 229 TYR 0.023 0.001 TYR G 33 PHE 0.009 0.001 PHE D 610 TRP 0.009 0.001 TRP H 36 HIS 0.004 0.001 HIS E 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (17943) covalent geometry : angle 0.62300 / 0.33 (24318) SS BOND : bond 0.01995 / 1.02 ( 21) SS BOND : angle 1.83022 / 1.04 ( 42) hydrogen bonds : bond 0.04238 / 2.81 ( 675) hydrogen bonds : angle 5.92884 / 4.14 ( 1935) link_BETA1-4 : bond 0.00371 / 0.21 ( 9) link_BETA1-4 : angle 1.68517 / 0.93 ( 27) link_NAG-ASN : bond 0.00293 / 0.16 ( 24) link_NAG-ASN : angle 1.58656 / 1.00 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.088 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: A 18 ASP cc_start: 0.9397 (m-30) cc_final: 0.8718 (p0) REVERT: A 88 ASN cc_start: 0.9379 (m-40) cc_final: 0.8978 (t0) REVERT: A 180 TRP cc_start: 0.8778 (p90) cc_final: 0.8480 (p90) outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 0.0829 time to fit residues: 7.5601 Evaluate side-chains 56 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.136 Evaluate side-chains 47 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.082 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: F 575 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7450 (ptt180) REVERT: F 578 GLU cc_start: 0.8852 (tt0) cc_final: 0.8445 (tt0) REVERT: F 591 ILE cc_start: 0.8186 (mm) cc_final: 0.7795 (tt) REVERT: F 601 LEU cc_start: 0.8036 (tp) cc_final: 0.7713 (tt) REVERT: F 603 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9032 (tp30) REVERT: F 616 LYS cc_start: 0.9591 (ttmt) cc_final: 0.9351 (ttmm) REVERT: F 620 GLU cc_start: 0.8991 (tp30) cc_final: 0.8717 (tp30) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1145 time to fit residues: 6.0548 Evaluate side-chains 39 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.072 Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.092 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: H 152 PHE cc_start: 0.7706 (p90) cc_final: 0.7354 (p90) REVERT: H 207 MET cc_start: 0.7716 (mpp) cc_final: 0.7385 (mpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1426 time to fit residues: 4.8975 Evaluate side-chains 23 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.089 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 28 optimal weight: 0.0020 chunk 115 optimal weight: 0.0870 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 0.0770 chunk 186 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 112 optimal weight: 0.0770 chunk 183 optimal weight: 6.9990 overall best weight: 0.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085951 restraints weight = 23428.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.090312 restraints weight = 11533.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.093322 restraints weight = 6549.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.095328 restraints weight = 4033.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.096728 restraints weight = 2629.162| |-----------------------------------------------------------------------------| r_work (final): 0.3555 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.103591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090248 restraints weight = 13554.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.094267 restraints weight = 6533.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.096671 restraints weight = 3591.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.098270 restraints weight = 2202.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.099188 restraints weight = 1456.838| |-----------------------------------------------------------------------------| r_work (final): 0.3773 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.075952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.066879 restraints weight = 29165.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.069665 restraints weight = 13697.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.071490 restraints weight = 7802.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.072627 restraints weight = 4894.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.073474 restraints weight = 3351.869| |-----------------------------------------------------------------------------| r_work (final): 0.3677 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.072145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.070419 restraints weight = 359.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.071400 restraints weight = 124.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.071777 restraints weight = 47.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.071961 restraints weight = 21.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.072005 restraints weight = 9.772 | |-----------------------------------------------------------------------------| r_work (final): 0.3020 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.086809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.083712 restraints weight = 226.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.084857 restraints weight = 124.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.085830 restraints weight = 78.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.086137 restraints weight = 34.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.086259 restraints weight = 12.266| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.6764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17997 Z= 0.122 Angle : 0.602 7.575 24459 Z= 0.323 Chirality : 0.043 0.149 2694 Planarity : 0.005 0.044 3132 Dihedral : 5.739 33.550 3075 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.05 (0.17), residues: 2172 helix: 1.37 (0.27), residues: 339 sheet: -1.81 (0.21), residues: 525 loop : -1.99 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 229 TYR 0.025 0.002 TYR H 33 PHE 0.012 0.001 PHE D 610 TRP 0.008 0.001 TRP H 242 HIS 0.004 0.001 HIS C 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17943) covalent geometry : angle 0.59225 / 0.32 (24318) SS BOND : bond 0.02007 / 1.00 ( 21) SS BOND : angle 1.76365 / 0.99 ( 42) hydrogen bonds : bond 0.04086 / 2.72 ( 675) hydrogen bonds : angle 5.79558 / 4.04 ( 1935) link_BETA1-4 : bond 0.00383 / 0.20 ( 9) link_BETA1-4 : angle 1.43593 / 0.81 ( 27) link_NAG-ASN : bond 0.00277 / 0.16 ( 24) link_NAG-ASN : angle 1.50308 / 0.95 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.132 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: E 18 ASP cc_start: 0.9564 (m-30) cc_final: 0.9174 (p0) REVERT: E 88 ASN cc_start: 0.9398 (m-40) cc_final: 0.8906 (t0) REVERT: E 103 GLU cc_start: 0.8305 (mp0) cc_final: 0.7828 (pt0) REVERT: E 180 TRP cc_start: 0.8539 (p90) cc_final: 0.8199 (p90) REVERT: E 244 ILE cc_start: 0.8292 (mt) cc_final: 0.7422 (mp) REVERT: E 245 PHE cc_start: 0.9215 (m-80) cc_final: 0.8720 (m-80) REVERT: E 246 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7694 (mp0) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.0976 time to fit residues: 8.0952 Evaluate side-chains 56 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.090 Evaluate side-chains 44 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.076 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: F 575 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7465 (ptt180) REVERT: F 578 GLU cc_start: 0.8845 (tt0) cc_final: 0.8614 (tt0) REVERT: F 591 ILE cc_start: 0.8174 (mm) cc_final: 0.7771 (tt) REVERT: F 601 LEU cc_start: 0.8060 (tp) cc_final: 0.7265 (tt) REVERT: F 603 GLU cc_start: 0.9476 (mm-30) cc_final: 0.8825 (tp30) REVERT: F 605 GLU cc_start: 0.6187 (mt-10) cc_final: 0.5695 (mp0) REVERT: F 616 LYS cc_start: 0.9597 (ttmt) cc_final: 0.9364 (ttmm) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1244 time to fit residues: 6.1030 Evaluate side-chains 36 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.075 Evaluate side-chains 31 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.115 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: H 100 PHE cc_start: 0.7227 (m-80) cc_final: 0.7021 (m-80) REVERT: H 152 PHE cc_start: 0.7673 (p90) cc_final: 0.7333 (p90) REVERT: H 207 MET cc_start: 0.8055 (mpp) cc_final: 0.7777 (mpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1407 time to fit residues: 4.9423 Evaluate side-chains 21 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.092 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 116 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 146 optimal weight: 0.0370 chunk 91 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 152 optimal weight: 0.4980 chunk 100 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.101238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086776 restraints weight = 22228.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.091149 restraints weight = 10734.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.094085 restraints weight = 6019.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.096111 restraints weight = 3673.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.097480 restraints weight = 2356.706| |-----------------------------------------------------------------------------| r_work (final): 0.3566 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.142311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.135969 restraints weight = 20668.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.137786 restraints weight = 9470.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.138833 restraints weight = 5020.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.139345 restraints weight = 2844.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.139673 restraints weight = 1922.103| |-----------------------------------------------------------------------------| r_work (final): 0.3786 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.075061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.064320 restraints weight = 28214.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.067597 restraints weight = 13688.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.069708 restraints weight = 7810.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.071065 restraints weight = 4909.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.072053 restraints weight = 3364.422| |-----------------------------------------------------------------------------| r_work (final): 0.3660 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.064919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.063448 restraints weight = 323.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.064185 restraints weight = 105.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.064538 restraints weight = 46.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.064701 restraints weight = 22.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.064790 restraints weight = 11.710| |-----------------------------------------------------------------------------| r_work (final): 0.2858 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.086541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.084034 restraints weight = 191.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.085317 restraints weight = 103.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.085907 restraints weight = 50.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.086017 restraints weight = 13.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.086027 restraints weight = 3.724 | |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.6934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17997 Z= 0.133 Angle : 0.612 8.753 24459 Z= 0.333 Chirality : 0.043 0.173 2694 Planarity : 0.005 0.076 3132 Dihedral : 5.664 32.485 3075 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.09 (0.17), residues: 2172 helix: 1.28 (0.27), residues: 345 sheet: -1.88 (0.20), residues: 543 loop : -1.99 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 229 TYR 0.026 0.002 TYR H 33 PHE 0.018 0.001 PHE G 63 TRP 0.021 0.002 TRP D 514 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (17943) covalent geometry : angle 0.60225 / 0.33 (24318) SS BOND : bond 0.02178 / 1.13 ( 21) SS BOND : angle 1.75385 / 0.97 ( 42) hydrogen bonds : bond 0.04219 / 2.80 ( 675) hydrogen bonds : angle 6.08912 / 4.27 ( 1935) link_BETA1-4 : bond 0.00450 / 0.24 ( 9) link_BETA1-4 : angle 1.46150 / 0.83 ( 27) link_NAG-ASN : bond 0.00395 / 0.22 ( 24) link_NAG-ASN : angle 1.47975 / 0.92 ( 72) =============================================================================== Job complete usr+sys time: 2628.07 seconds wall clock time: 46 minutes 22.62 seconds (2782.62 seconds total)