Starting phenix.real_space_refine on Mon Sep 14 23:01:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5uk1_8563/09_2026/5uk1_8563_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5uk1_8563/09_2026/5uk1_8563.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 { model { file = "/net/cci-nas-00/data/ceres_data/5uk1_8563/09_2026/5uk1_8563_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5uk1_8563/09_2026/5uk1_8563_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5uk1_8563/09_2026/5uk1_8563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5uk1_8563/09_2026/5uk1_8563.map" } 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= 0.069 sd= 0.375 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.38, per 1000 atoms: 0.16 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=2.05 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 648 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 637 " distance=1.96 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS D 644 " - pdb=" SG CYS D 648 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 637 " distance=2.06 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.04 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.02 Simple disulfide: pdb=" SG CYS F 644 " - pdb=" SG CYS F 648 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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: 2.92 Conformation dependent library (CDL) restraints added in 928.1 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 48 sheets defined 18.4% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 removed outlier: 4.083A 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: 4.166A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.994A 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: 3.803A pdb=" N GLN B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 3.919A 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: 4.084A 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: 4.166A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.995A 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: 3.802A pdb=" N GLN D 625 " --> pdb=" O LYS D 621 " (cutoff:3.500A) removed outlier: 3.918A 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: 4.084A 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: 4.166A pdb=" N TRP E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.994A 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: 3.803A pdb=" N GLN F 625 " --> pdb=" O LYS F 621 " (cutoff:3.500A) removed outlier: 3.919A 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 removed outlier: 3.535A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.534A pdb=" N PHE H 84 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.534A pdb=" N PHE I 84 " --> pdb=" O PRO I 81 " (cutoff:3.500A) 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: 3.990A pdb=" N CYS B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 22 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 47 through 48 removed outlier: 5.917A pdb=" N LEU A 47 " --> pdb=" O ALA A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.601A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 140 removed outlier: 4.706A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 153 removed outlier: 8.152A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 removed outlier: 8.152A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.921A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 531 through 536 removed outlier: 3.990A pdb=" N CYS D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB6, first strand: chain 'C' and resid 47 through 48 removed outlier: 5.916A pdb=" N LEU C 47 " --> pdb=" O ALA C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.601A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB9, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.706A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'C' and resid 287 through 289 removed outlier: 3.921A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 531 through 536 removed outlier: 3.990A pdb=" N CYS F 637 " --> pdb=" O ILE F 633 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AC7, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AC8, first strand: chain 'E' and resid 47 through 48 removed outlier: 5.916A pdb=" N LEU E 47 " --> pdb=" O ALA E 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.602A pdb=" N LEU E 54 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD2, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.707A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'E' and resid 287 through 289 removed outlier: 3.922A pdb=" N CYS E 282 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AE1, first strand: chain 'G' and resid 129 through 132 removed outlier: 5.809A pdb=" N GLY G 141 " --> pdb=" O ASN G 209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 136 through 137 removed outlier: 6.991A pdb=" N MET G 159 " --> pdb=" O GLY G 175 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY G 175 " --> pdb=" O MET G 159 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP G 161 " --> pdb=" O VAL G 173 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN H 38 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU H 47 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE6, first strand: chain 'H' and resid 129 through 132 removed outlier: 5.810A pdb=" N GLY H 141 " --> pdb=" O ASN H 209 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 136 through 137 removed outlier: 6.992A pdb=" N MET H 159 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY H 175 " --> pdb=" O MET H 159 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP H 161 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AF2, first strand: chain 'I' and resid 129 through 132 removed outlier: 5.809A pdb=" N GLY I 141 " --> pdb=" O ASN I 209 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 136 through 137 removed outlier: 6.991A pdb=" N MET I 159 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY I 175 " --> pdb=" O MET I 159 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP I 161 " --> pdb=" O VAL I 173 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 1845 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: 7.45 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 16395 1.01 - 1.21: 6 1.21 - 1.42: 7627 1.42 - 1.62: 10214 1.62 - 1.82: 102 Bond restraints: 34344 Sorted by residual: bond pdb=" CA TRP I 36 " pdb=" CB TRP I 36 " ideal model delta sigma weight residual 1.532 1.483 0.048 1.82e-02 3.02e+03 7.03e+00 bond pdb=" CA TRP H 36 " pdb=" CB TRP H 36 " ideal model delta sigma weight residual 1.532 1.484 0.048 1.82e-02 3.02e+03 6.87e+00 bond pdb=" CA TRP G 36 " pdb=" CB TRP G 36 " ideal model delta sigma weight residual 1.532 1.484 0.047 1.82e-02 3.02e+03 6.80e+00 bond pdb=" NE1 TRP C 153 " pdb=" HE1 TRP C 153 " ideal model delta sigma weight residual 0.860 0.809 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" NE1 TRP A 153 " pdb=" HE1 TRP A 153 " ideal model delta sigma weight residual 0.860 0.810 0.050 2.00e-02 2.50e+03 6.34e+00 ... (remaining 34339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 55733 2.10 - 4.20: 5029 4.20 - 6.30: 665 6.30 - 8.40: 108 8.40 - 10.51: 22 Bond angle restraints: 61557 Sorted by residual: angle pdb=" C GLU I 1 " pdb=" N ILE I 2 " pdb=" CA ILE I 2 " ideal model delta sigma weight residual 120.35 127.76 -7.41 1.39e+00 5.18e-01 2.84e+01 angle pdb=" C GLU G 1 " pdb=" N ILE G 2 " pdb=" CA ILE G 2 " ideal model delta sigma weight residual 120.35 127.73 -7.38 1.39e+00 5.18e-01 2.82e+01 angle pdb=" C GLU H 1 " pdb=" N ILE H 2 " pdb=" CA ILE H 2 " ideal model delta sigma weight residual 120.35 127.69 -7.34 1.39e+00 5.18e-01 2.79e+01 angle pdb=" N SER H 30 " pdb=" CA SER H 30 " pdb=" C SER H 30 " ideal model delta sigma weight residual 113.28 121.54 -8.26 1.57e+00 4.06e-01 2.77e+01 angle pdb=" N SER I 30 " pdb=" CA SER I 30 " pdb=" C SER I 30 " ideal model delta sigma weight residual 113.28 121.53 -8.25 1.57e+00 4.06e-01 2.76e+01 ... (remaining 61552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.35: 15607 19.35 - 38.71: 867 38.71 - 58.06: 271 58.06 - 77.42: 46 77.42 - 96.77: 15 Dihedral angle restraints: 16806 sinusoidal: 9345 harmonic: 7461 Sorted by residual: dihedral pdb=" CA GLY I 58 " pdb=" C GLY I 58 " pdb=" N ILE I 59 " pdb=" CA ILE I 59 " ideal model delta harmonic sigma weight residual -180.00 -147.43 -32.57 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA GLY H 58 " pdb=" C GLY H 58 " pdb=" N ILE H 59 " pdb=" CA ILE H 59 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA GLY G 58 " pdb=" C GLY G 58 " pdb=" N ILE G 59 " pdb=" CA ILE G 59 " ideal model delta harmonic sigma weight residual -180.00 -147.51 -32.49 0 5.00e+00 4.00e-02 4.22e+01 ... (remaining 16803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2235 0.081 - 0.163: 398 0.163 - 0.244: 43 0.244 - 0.326: 11 0.326 - 0.407: 7 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 -2.24 -0.16 2.00e-02 2.50e+03 6.76e+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 -2.24 -0.16 2.00e-02 2.50e+03 6.66e+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 -2.24 -0.16 2.00e-02 2.50e+03 6.53e+01 ... (remaining 2691 not shown) Planarity restraints: 5244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 248 " -0.149 2.00e-02 2.50e+03 1.75e-01 4.60e+02 pdb=" CG ASN E 248 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN E 248 " 0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN E 248 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN E 248 " 0.260 2.00e-02 2.50e+03 pdb="HD22 ASN E 248 " -0.263 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 248 " -0.148 2.00e-02 2.50e+03 1.74e-01 4.56e+02 pdb=" CG ASN A 248 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 248 " 0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN A 248 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 248 " 0.259 2.00e-02 2.50e+03 pdb="HD22 ASN A 248 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 248 " 0.148 2.00e-02 2.50e+03 1.74e-01 4.53e+02 pdb=" CG ASN C 248 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 248 " -0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN C 248 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 248 " -0.258 2.00e-02 2.50e+03 pdb="HD22 ASN C 248 " 0.261 2.00e-02 2.50e+03 ... (remaining 5241 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 7614 2.31 - 2.88: 77229 2.88 - 3.45: 86327 3.45 - 4.03: 119135 4.03 - 4.60: 178874 Nonbonded interactions: 469179 Sorted by model distance: nonbonded pdb=" H GLY H 140 " pdb=" O LEU H 210 " model vdw 1.735 2.450 nonbonded pdb=" H THR E 31 " pdb=" O LEU E 321 " model vdw 1.736 2.450 nonbonded pdb=" H THR C 31 " pdb=" O LEU C 321 " model vdw 1.736 2.450 nonbonded pdb=" H THR A 31 " pdb=" O LEU A 321 " model vdw 1.737 2.450 nonbonded pdb=" H GLY G 140 " pdb=" O LEU G 210 " model vdw 1.738 2.450 ... (remaining 469174 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: 0.06 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: 0.080 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: 0.180 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.020 Find NCS groups from input model: 0.250 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 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 0.083 17997 Z= 0.467 Angle : 1.305 9.783 24459 Z= 0.751 Chirality : 0.065 0.407 2694 Planarity : 0.009 0.082 3132 Dihedral : 12.045 96.773 7023 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.06 % Favored : 91.80 % Rotamer: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.57 % 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: -3.97 (0.14), residues: 2172 helix: -1.38 (0.22), residues: 348 sheet: -2.97 (0.17), residues: 546 loop : -2.94 (0.14), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG H 222 TYR 0.032 0.005 TYR C 95 PHE 0.036 0.004 PHE D 509 TRP 0.029 0.005 TRP A 127 HIS 0.019 0.005 HIS D 611 Details of bonding type rmsd/Z covalent geometry : bond 0.01011 / 0.47 (17943) covalent geometry : angle 1.28106 / 0.75 (24318) SS BOND : bond 0.01864 / 0.90 ( 21) SS BOND : angle 2.19512 / 1.41 ( 42) hydrogen bonds : bond 0.10955 / 7.12 ( 654) hydrogen bonds : angle 11.13390 / 7.79 ( 1845) link_BETA1-4 : bond 0.01125 / 0.53 ( 9) link_BETA1-4 : angle 4.08142 / 2.58 ( 27) link_NAG-ASN : bond 0.01180 / 0.71 ( 24) link_NAG-ASN : angle 3.93090 / 2.45 ( 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 70 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.142 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: A 35 ASN cc_start: 0.8881 (t0) cc_final: 0.8657 (t0) REVERT: A 83 ILE cc_start: 0.9525 (mt) cc_final: 0.9037 (mt) REVERT: A 84 VAL cc_start: 0.8884 (t) cc_final: 0.8370 (t) REVERT: A 184 HIS cc_start: 0.8971 (m90) cc_final: 0.8444 (m-70) REVERT: A 212 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7656 (mmtm) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.1463 time to fit residues: 11.9312 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 : 0.106 Evaluate side-chains 78 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.9504 (tp40) cc_final: 0.9099 (tp-100) REVERT: B 576 ARG cc_start: 0.8551 (mtm180) cc_final: 0.8188 (ttt180) REVERT: B 588 PHE cc_start: 0.8947 (m-80) cc_final: 0.8646 (m-80) REVERT: B 598 LEU cc_start: 0.9568 (mt) cc_final: 0.9019 (mt) REVERT: B 619 TYR cc_start: 0.7929 (t80) cc_final: 0.7710 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1671 time to fit residues: 13.9377 Evaluate side-chains 45 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.047 Evaluate side-chains 55 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 143 LEU cc_start: 0.9468 (tp) cc_final: 0.9063 (pp) REVERT: G 204 TYR cc_start: 0.8539 (m-80) cc_final: 0.7956 (m-80) REVERT: G 219 PHE cc_start: 0.8743 (m-80) cc_final: 0.7782 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2088 time to fit residues: 12.4519 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 : 0.090 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: 9.9990 chunk 194 optimal weight: 0.0980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS B 617 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 = 0.3332 r_free = 0.3332 target = 0.056806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.044500 restraints weight = 43510.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.047521 restraints weight = 22218.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049777 restraints weight = 13197.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.051427 restraints weight = 8532.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.052733 restraints weight = 5835.116| |-----------------------------------------------------------------------------| r_work (final): 0.3235 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.071632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.056829 restraints weight = 22042.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.060148 restraints weight = 12377.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.062672 restraints weight = 7847.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.064534 restraints weight = 5325.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.065903 restraints weight = 3758.329| |-----------------------------------------------------------------------------| r_work (final): 0.3631 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.062919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.048985 restraints weight = 36679.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.052627 restraints weight = 20226.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.055366 restraints weight = 12469.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.057359 restraints weight = 8175.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.058773 restraints weight = 5529.227| |-----------------------------------------------------------------------------| r_work (final): 0.3609 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.038018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.035737 restraints weight = 663.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.036111 restraints weight = 388.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.036412 restraints weight = 277.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.036613 restraints weight = 214.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.036761 restraints weight = 174.934| |-----------------------------------------------------------------------------| r_work (final): 0.2366 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.054931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054479 restraints weight = 463.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054772 restraints weight = 109.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.054867 restraints weight = 33.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054912 restraints weight = 12.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.054906 restraints weight = 4.178 | |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 17997 Z= 0.251 Angle : 0.927 12.804 24459 Z= 0.496 Chirality : 0.048 0.226 2694 Planarity : 0.015 0.403 3132 Dihedral : 11.240 70.491 3075 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.32 % Allowed : 2.27 % Favored : 97.41 % 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: -3.66 (0.14), residues: 2172 helix: -0.75 (0.26), residues: 336 sheet: -2.75 (0.18), residues: 507 loop : -2.88 (0.13), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG F 575 TYR 0.025 0.002 TYR A 102 PHE 0.022 0.002 PHE B 509 TRP 0.015 0.002 TRP C 127 HIS 0.017 0.002 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.25 (17943) covalent geometry : angle 0.90049 / 0.49 (24318) SS BOND : bond 0.01888 / 0.98 ( 21) SS BOND : angle 1.38874 / 0.84 ( 42) hydrogen bonds : bond 0.08505 / 6.04 ( 654) hydrogen bonds : angle 8.63627 / 6.00 ( 1845) link_BETA1-4 : bond 0.01496 / 0.75 ( 9) link_BETA1-4 : angle 4.95647 / 2.72 ( 27) link_NAG-ASN : bond 0.00790 / 0.48 ( 24) link_NAG-ASN : angle 2.79130 / 1.80 ( 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 58 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.136 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: C 39 ASP cc_start: 0.9312 (t0) cc_final: 0.8993 (t0) REVERT: C 231 ASN cc_start: 0.9678 (m-40) cc_final: 0.9363 (t0) outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.0807 time to fit residues: 6.0979 Evaluate side-chains 43 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.088 Evaluate side-chains 59 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 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: symmetry clash REVERT: B 542 GLN cc_start: 0.9748 (tp40) cc_final: 0.9477 (tp-100) REVERT: B 576 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8379 (ttt180) REVERT: B 590 ASP cc_start: 0.8988 (m-30) cc_final: 0.8782 (m-30) REVERT: B 619 TYR cc_start: 0.8804 (t80) cc_final: 0.8602 (t80) REVERT: B 646 ASP cc_start: 0.9357 (p0) cc_final: 0.8995 (p0) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1097 time to fit residues: 7.2802 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 : 0.083 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 : 0.071 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 143 LEU cc_start: 0.9422 (tp) cc_final: 0.9114 (pp) REVERT: H 204 TYR cc_start: 0.8762 (m-80) cc_final: 0.8083 (m-80) REVERT: H 219 PHE cc_start: 0.9077 (m-80) cc_final: 0.8340 (m-80) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2499 time to fit residues: 10.3959 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 : 0.086 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: 0.0011 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 150 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 635 ASN C 32 HIS ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS C 296 GLN H 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.057129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.045864 restraints weight = 47028.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.048752 restraints weight = 23897.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.050929 restraints weight = 14105.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052494 restraints weight = 9006.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.053660 restraints weight = 6051.494| |-----------------------------------------------------------------------------| r_work (final): 0.3227 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.067988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.054345 restraints weight = 22579.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.057562 restraints weight = 12449.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.060027 restraints weight = 7833.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.061893 restraints weight = 5220.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.063348 restraints weight = 3634.090| |-----------------------------------------------------------------------------| r_work (final): 0.3407 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.066198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.048020 restraints weight = 30573.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.051517 restraints weight = 16692.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.054492 restraints weight = 10622.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.056876 restraints weight = 7108.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.058770 restraints weight = 4954.542| |-----------------------------------------------------------------------------| r_work (final): 0.3602 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2199 r_free = 0.2199 target = 0.032486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2182 r_free = 0.2182 target = 0.030424 restraints weight = 699.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2186 r_free = 0.2186 target = 0.030854 restraints weight = 391.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2187 r_free = 0.2187 target = 0.031130 restraints weight = 272.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2190 r_free = 0.2190 target = 0.031377 restraints weight = 205.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2189 r_free = 0.2189 target = 0.031531 restraints weight = 159.782| |-----------------------------------------------------------------------------| r_work (final): 0.2180 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.054394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052920 restraints weight = 227.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.053340 restraints weight = 96.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.053571 restraints weight = 47.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.053703 restraints weight = 25.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.053796 restraints weight = 14.963| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17997 Z= 0.194 Angle : 0.794 14.930 24459 Z= 0.427 Chirality : 0.045 0.299 2694 Planarity : 0.014 0.394 3132 Dihedral : 9.423 62.422 3075 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.65 % Allowed : 1.46 % Favored : 97.90 % 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: -3.49 (0.15), residues: 2172 helix: -0.67 (0.26), residues: 333 sheet: -2.65 (0.19), residues: 528 loop : -2.72 (0.14), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 311 TYR 0.022 0.002 TYR I 33 PHE 0.016 0.002 PHE D 610 TRP 0.013 0.002 TRP C 127 HIS 0.012 0.002 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (17943) covalent geometry : angle 0.77886 / 0.42 (24318) SS BOND : bond 0.01839 / 0.94 ( 21) SS BOND : angle 1.13909 / 0.74 ( 42) hydrogen bonds : bond 0.05988 / 4.14 ( 654) hydrogen bonds : angle 8.05497 / 5.57 ( 1845) link_BETA1-4 : bond 0.00841 / 0.44 ( 9) link_BETA1-4 : angle 2.91052 / 1.58 ( 27) link_NAG-ASN : bond 0.00807 / 0.49 ( 24) link_NAG-ASN : angle 2.35584 / 1.51 ( 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 46 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 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 outliers start: 2 outliers final: 2 residues processed: 45 average time/residue: 0.0863 time to fit residues: 5.0681 Evaluate side-chains 40 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.134 Evaluate side-chains 59 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 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: 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: 0.9770 (tp40) cc_final: 0.9551 (tp-100) REVERT: B 595 ASN cc_start: 0.9683 (m-40) cc_final: 0.9435 (p0) REVERT: B 662 TYR cc_start: 0.9130 (m-80) cc_final: 0.8901 (m-80) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1092 time to fit residues: 7.2047 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 : 0.079 Evaluate side-chains 40 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 204 TYR cc_start: 0.9335 (m-80) cc_final: 0.8983 (m-80) REVERT: G 218 TYR cc_start: 0.9427 (m-80) cc_final: 0.9128 (m-80) REVERT: G 219 PHE cc_start: 0.9342 (m-80) cc_final: 0.8590 (m-80) REVERT: G 239 MET cc_start: 0.9555 (tpp) cc_final: 0.9299 (tpp) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.2840 time to fit residues: 12.1205 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 : 0.091 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 150 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 542 GLN B 546 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.055651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.044811 restraints weight = 49740.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047613 restraints weight = 25130.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.049719 restraints weight = 14774.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051210 restraints weight = 9389.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.052281 restraints weight = 6320.543| |-----------------------------------------------------------------------------| r_work (final): 0.3211 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.066856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.055212 restraints weight = 23805.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.057821 restraints weight = 13352.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.059801 restraints weight = 8602.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.061255 restraints weight = 5865.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.062294 restraints weight = 4199.143| |-----------------------------------------------------------------------------| r_work (final): 0.3384 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.064346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.045566 restraints weight = 30800.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.049854 restraints weight = 15968.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.053075 restraints weight = 9587.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.055483 restraints weight = 6230.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057273 restraints weight = 4278.584| |-----------------------------------------------------------------------------| r_work (final): 0.3586 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.036056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2223 r_free = 0.2223 target = 0.034013 restraints weight = 547.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2218 r_free = 0.2218 target = 0.034445 restraints weight = 311.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2219 r_free = 0.2219 target = 0.034768 restraints weight = 199.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2219 r_free = 0.2219 target = 0.034990 restraints weight = 148.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2219 r_free = 0.2219 target = 0.035174 restraints weight = 115.289| |-----------------------------------------------------------------------------| r_work (final): 0.2209 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.054982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.053339 restraints weight = 317.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.053734 restraints weight = 118.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.054028 restraints weight = 63.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.054190 restraints weight = 35.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.054284 restraints weight = 21.522| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 17997 Z= 0.226 Angle : 0.773 15.733 24459 Z= 0.419 Chirality : 0.043 0.180 2694 Planarity : 0.007 0.152 3132 Dihedral : 8.131 47.512 3075 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.67 % Favored : 90.19 % Rotamer: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % 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: -3.36 (0.15), residues: 2172 helix: -0.39 (0.27), residues: 327 sheet: -2.56 (0.20), residues: 534 loop : -2.68 (0.14), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 575 TYR 0.022 0.002 TYR H 33 PHE 0.016 0.002 PHE H 192 TRP 0.014 0.002 TRP C 127 HIS 0.009 0.002 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (17943) covalent geometry : angle 0.75896 / 0.42 (24318) SS BOND : bond 0.01860 / 0.96 ( 21) SS BOND : angle 1.17412 / 0.68 ( 42) hydrogen bonds : bond 0.05050 / 3.37 ( 654) hydrogen bonds : angle 7.85659 / 5.48 ( 1845) link_BETA1-4 : bond 0.00454 / 0.24 ( 9) link_BETA1-4 : angle 2.24604 / 1.24 ( 27) link_NAG-ASN : bond 0.00843 / 0.51 ( 24) link_NAG-ASN : angle 2.36405 / 1.51 ( 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 41 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 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: C 38 GLU cc_start: 0.7534 (tp30) cc_final: 0.6535 (tt0) REVERT: C 231 ASN cc_start: 0.9601 (m110) cc_final: 0.9177 (t0) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.0817 time to fit residues: 4.4780 Evaluate side-chains 33 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.153 Evaluate side-chains 50 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.9722 (tp-100) cc_final: 0.9498 (tp-100) REVERT: B 590 ASP cc_start: 0.9595 (m-30) cc_final: 0.9358 (m-30) REVERT: B 592 TRP cc_start: 0.8825 (m100) cc_final: 0.8037 (m-10) REVERT: B 595 ASN cc_start: 0.9456 (m-40) cc_final: 0.9137 (p0) REVERT: B 611 HIS cc_start: 0.9391 (m-70) cc_final: 0.9101 (m-70) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0960 time to fit residues: 5.4892 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 : 0.073 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 : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 143 LEU cc_start: 0.9329 (tp) cc_final: 0.9003 (pp) REVERT: G 218 TYR cc_start: 0.9264 (m-80) cc_final: 0.8909 (m-80) REVERT: G 219 PHE cc_start: 0.9321 (m-80) cc_final: 0.8419 (m-80) REVERT: G 239 MET cc_start: 0.9234 (tpp) cc_final: 0.8550 (tpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2963 time to fit residues: 11.3425 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 : 0.090 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: 0.0010 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 : 0.000 ------------------------------------------------------------------------------- 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: 4.9990 chunk 25 optimal weight: 0.1980 chunk 62 optimal weight: 30.0000 chunk 81 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 193 optimal weight: 0.0670 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 overall best weight: 2.8524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.055835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.044630 restraints weight = 47508.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.047476 restraints weight = 23526.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.049677 restraints weight = 13744.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.051264 restraints weight = 8706.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.052364 restraints weight = 5800.984| |-----------------------------------------------------------------------------| r_work (final): 0.3216 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.065775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.053010 restraints weight = 23321.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.055631 restraints weight = 12983.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.057660 restraints weight = 8313.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.059181 restraints weight = 5697.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.060383 restraints weight = 4126.172| |-----------------------------------------------------------------------------| r_work (final): 0.3359 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.094505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.083743 restraints weight = 54136.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.085907 restraints weight = 28220.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.087220 restraints weight = 16300.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.088055 restraints weight = 9999.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.088614 restraints weight = 6543.927| |-----------------------------------------------------------------------------| r_work (final): 0.3641 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.037668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.034978 restraints weight = 566.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.035493 restraints weight = 325.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.035787 restraints weight = 227.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.036020 restraints weight = 174.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.036219 restraints weight = 142.103| |-----------------------------------------------------------------------------| r_work (final): 0.2320 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.053053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.051786 restraints weight = 350.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.052209 restraints weight = 123.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.052403 restraints weight = 54.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.052547 restraints weight = 30.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.052599 restraints weight = 17.979| |-----------------------------------------------------------------------------| r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 17997 Z= 0.217 Angle : 0.722 6.831 24459 Z= 0.395 Chirality : 0.043 0.258 2694 Planarity : 0.007 0.087 3132 Dihedral : 7.726 48.730 3075 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % 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 : 0.00 % 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: -3.32 (0.15), residues: 2172 helix: -0.62 (0.26), residues: 345 sheet: -2.51 (0.20), residues: 498 loop : -2.62 (0.14), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 575 TYR 0.021 0.002 TYR I 33 PHE 0.013 0.002 PHE F 610 TRP 0.013 0.001 TRP A 127 HIS 0.006 0.002 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (17943) covalent geometry : angle 0.70958 / 0.39 (24318) SS BOND : bond 0.01862 / 0.97 ( 21) SS BOND : angle 1.19878 / 0.75 ( 42) hydrogen bonds : bond 0.04773 / 3.18 ( 654) hydrogen bonds : angle 7.45894 / 5.19 ( 1845) link_BETA1-4 : bond 0.00352 / 0.21 ( 9) link_BETA1-4 : angle 2.22173 / 1.23 ( 27) link_NAG-ASN : bond 0.00814 / 0.49 ( 24) link_NAG-ASN : angle 2.14015 / 1.36 ( 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 41 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 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: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.7484 (tp30) cc_final: 0.6504 (tt0) REVERT: C 231 ASN cc_start: 0.9589 (m110) cc_final: 0.9340 (t0) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.0592 time to fit residues: 3.5349 Evaluate side-chains 35 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.140 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 : 0.076 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: 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: 0.9689 (tp-100) cc_final: 0.9459 (tp-100) REVERT: B 557 GLU cc_start: 0.8858 (pt0) cc_final: 0.8555 (pt0) REVERT: B 570 PHE cc_start: 0.5178 (m-80) cc_final: 0.4746 (m-80) REVERT: B 585 ASP cc_start: 0.9410 (m-30) cc_final: 0.9183 (m-30) REVERT: B 590 ASP cc_start: 0.9644 (m-30) cc_final: 0.9426 (m-30) REVERT: B 592 TRP cc_start: 0.8673 (m100) cc_final: 0.7539 (t60) REVERT: B 595 ASN cc_start: 0.9401 (m-40) cc_final: 0.9084 (p0) REVERT: B 611 HIS cc_start: 0.9380 (m-70) cc_final: 0.9116 (m-70) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0871 time to fit residues: 5.2233 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 : 0.057 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 : 0.098 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 143 LEU cc_start: 0.9362 (tp) cc_final: 0.9025 (pp) REVERT: G 200 LYS cc_start: 0.9392 (mmpt) cc_final: 0.9182 (mmmt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2764 time to fit residues: 10.6597 Evaluate side-chains 29 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 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: 0.0008 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 : 0.000 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: 2.9990 chunk 174 optimal weight: 0.1980 chunk 171 optimal weight: 0.2980 chunk 204 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 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 = 0.3310 r_free = 0.3310 target = 0.056053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.044793 restraints weight = 48300.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.047743 restraints weight = 23111.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050011 restraints weight = 13309.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.051569 restraints weight = 8371.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.052699 restraints weight = 5561.320| |-----------------------------------------------------------------------------| r_work (final): 0.3209 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.066155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.053851 restraints weight = 22762.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056447 restraints weight = 13058.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.058444 restraints weight = 8492.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059927 restraints weight = 5888.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.061134 restraints weight = 4270.653| |-----------------------------------------------------------------------------| r_work (final): 0.3378 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.060644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.045793 restraints weight = 33019.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.049469 restraints weight = 18337.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.052242 restraints weight = 11330.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.054264 restraints weight = 7499.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.055745 restraints weight = 5219.504| |-----------------------------------------------------------------------------| r_work (final): 0.3487 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.042735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.039376 restraints weight = 586.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.039945 restraints weight = 433.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.040394 restraints weight = 338.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.040738 restraints weight = 279.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.041000 restraints weight = 234.196| |-----------------------------------------------------------------------------| r_work (final): 0.2362 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.052638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.051471 restraints weight = 321.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.051868 restraints weight = 127.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.052077 restraints weight = 68.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.052242 restraints weight = 41.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.052326 restraints weight = 24.846| |-----------------------------------------------------------------------------| r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17997 Z= 0.161 Angle : 0.676 6.750 24459 Z= 0.369 Chirality : 0.043 0.186 2694 Planarity : 0.006 0.075 3132 Dihedral : 7.306 48.654 3075 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % 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: -3.19 (0.16), residues: 2172 helix: -0.27 (0.27), residues: 345 sheet: -2.43 (0.19), residues: 534 loop : -2.60 (0.15), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 575 TYR 0.022 0.002 TYR G 33 PHE 0.013 0.002 PHE B 610 TRP 0.012 0.001 TRP C 127 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (17943) covalent geometry : angle 0.66367 / 0.37 (24318) SS BOND : bond 0.01906 / 0.98 ( 21) SS BOND : angle 1.41626 / 0.81 ( 42) hydrogen bonds : bond 0.04567 / 3.06 ( 654) hydrogen bonds : angle 7.12115 / 4.94 ( 1845) link_BETA1-4 : bond 0.00488 / 0.26 ( 9) link_BETA1-4 : angle 1.79312 / 1.00 ( 27) link_NAG-ASN : bond 0.00808 / 0.49 ( 24) link_NAG-ASN : angle 1.97241 / 1.25 ( 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 37 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.148 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: C 38 GLU cc_start: 0.7482 (tp30) cc_final: 0.7198 (tm-30) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.0601 time to fit residues: 3.2409 Evaluate side-chains 29 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.140 Evaluate side-chains 50 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.9644 (tp-100) cc_final: 0.9406 (tp-100) REVERT: B 557 GLU cc_start: 0.8870 (pt0) cc_final: 0.8562 (pt0) REVERT: B 585 ASP cc_start: 0.9413 (m-30) cc_final: 0.9207 (m-30) REVERT: B 586 ASP cc_start: 0.9358 (m-30) cc_final: 0.9158 (m-30) REVERT: B 592 TRP cc_start: 0.8638 (m100) cc_final: 0.7592 (t60) REVERT: B 595 ASN cc_start: 0.9395 (m-40) cc_final: 0.9105 (p0) REVERT: B 611 HIS cc_start: 0.9372 (m-70) cc_final: 0.9087 (m-70) REVERT: B 620 GLU cc_start: 0.9726 (mm-30) cc_final: 0.9344 (mm-30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0961 time to fit residues: 5.5085 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 : 0.082 Evaluate side-chains 34 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.9408 (mmpt) cc_final: 0.9185 (mmmt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2793 time to fit residues: 10.1398 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 : 0.158 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 : 0.000 ------------------------------------------------------------------------------- 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: 9.9990 chunk 99 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 595 ASN B 614 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.053843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.043398 restraints weight = 51300.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.046178 restraints weight = 25406.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.048262 restraints weight = 14670.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.049674 restraints weight = 9210.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050703 restraints weight = 6126.130| |-----------------------------------------------------------------------------| r_work (final): 0.3169 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.065358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.054129 restraints weight = 23553.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.056573 restraints weight = 13700.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.058442 restraints weight = 8938.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.059959 restraints weight = 6147.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.060978 restraints weight = 4344.195| |-----------------------------------------------------------------------------| r_work (final): 0.3452 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.058893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.045582 restraints weight = 39034.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.048855 restraints weight = 21663.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.051260 restraints weight = 13574.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.053104 restraints weight = 9131.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.054446 restraints weight = 6391.002| |-----------------------------------------------------------------------------| r_work (final): 0.3437 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2378 r_free = 0.2378 target = 0.042408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2291 r_free = 0.2291 target = 0.038022 restraints weight = 425.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2298 r_free = 0.2298 target = 0.038484 restraints weight = 312.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2307 r_free = 0.2307 target = 0.038813 restraints weight = 255.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2313 r_free = 0.2313 target = 0.039109 restraints weight = 220.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.039348 restraints weight = 190.899| |-----------------------------------------------------------------------------| r_work (final): 0.2300 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.053139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.052774 restraints weight = 474.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.052974 restraints weight = 98.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.053066 restraints weight = 34.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.053106 restraints weight = 13.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.053122 restraints weight = 5.497 | |-----------------------------------------------------------------------------| r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17997 Z= 0.261 Angle : 0.745 6.589 24459 Z= 0.404 Chirality : 0.043 0.163 2694 Planarity : 0.006 0.073 3132 Dihedral : 7.305 47.979 3075 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % 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: -3.23 (0.16), residues: 2172 helix: -0.10 (0.28), residues: 327 sheet: -2.56 (0.20), residues: 495 loop : -2.63 (0.14), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 575 TYR 0.020 0.002 TYR C 161 PHE 0.020 0.002 PHE C 213 TRP 0.014 0.002 TRP A 127 HIS 0.010 0.002 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.26 (17943) covalent geometry : angle 0.73390 / 0.40 (24318) SS BOND : bond 0.01888 / 0.97 ( 21) SS BOND : angle 1.35682 / 0.81 ( 42) hydrogen bonds : bond 0.04752 / 3.18 ( 654) hydrogen bonds : angle 7.11301 / 4.94 ( 1845) link_BETA1-4 : bond 0.00373 / 0.19 ( 9) link_BETA1-4 : angle 1.82050 / 1.02 ( 27) link_NAG-ASN : bond 0.00883 / 0.53 ( 24) link_NAG-ASN : angle 2.08992 / 1.32 ( 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 35 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.140 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: C 38 GLU cc_start: 0.7624 (tp30) cc_final: 0.6588 (tt0) REVERT: C 245 PHE cc_start: 0.9490 (m-80) cc_final: 0.9228 (m-80) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.0641 time to fit residues: 3.2741 Evaluate side-chains 28 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.147 Evaluate side-chains 48 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 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: B 542 GLN cc_start: 0.9476 (tp-100) cc_final: 0.9136 (tp-100) REVERT: B 557 GLU cc_start: 0.8555 (pt0) cc_final: 0.8240 (pt0) REVERT: B 583 LYS cc_start: 0.8646 (tttt) cc_final: 0.8414 (tttt) REVERT: B 585 ASP cc_start: 0.9173 (m-30) cc_final: 0.8941 (m-30) REVERT: B 586 ASP cc_start: 0.9330 (m-30) cc_final: 0.9075 (m-30) REVERT: B 592 TRP cc_start: 0.8538 (m100) cc_final: 0.7446 (t60) REVERT: B 595 ASN cc_start: 0.9294 (m110) cc_final: 0.9029 (p0) REVERT: B 611 HIS cc_start: 0.9130 (m-70) cc_final: 0.8853 (m-70) REVERT: B 617 ASN cc_start: 0.9258 (m110) cc_final: 0.8861 (m110) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0994 time to fit residues: 5.4524 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 : 0.080 Evaluate side-chains 34 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 143 LEU cc_start: 0.9453 (tp) cc_final: 0.9134 (pp) REVERT: G 159 MET cc_start: 0.9230 (mmp) cc_final: 0.8888 (mmp) REVERT: G 200 LYS cc_start: 0.9434 (mmpt) cc_final: 0.9211 (mmmt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2485 time to fit residues: 9.1418 Evaluate side-chains 29 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.101 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: 0.0010 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 63 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043830 restraints weight = 52143.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.046690 restraints weight = 26057.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.048803 restraints weight = 15203.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.050284 restraints weight = 9612.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.051330 restraints weight = 6349.354| |-----------------------------------------------------------------------------| r_work (final): 0.3203 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.061541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.049042 restraints weight = 23987.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.051785 restraints weight = 12743.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053909 restraints weight = 8004.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055523 restraints weight = 5420.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.056810 restraints weight = 3864.503| |-----------------------------------------------------------------------------| r_work (final): 0.3379 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.057581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.045123 restraints weight = 36028.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.048528 restraints weight = 19554.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.050967 restraints weight = 11974.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.052632 restraints weight = 7764.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.053928 restraints weight = 5332.558| |-----------------------------------------------------------------------------| r_work (final): 0.3468 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.040578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.037773 restraints weight = 656.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.038405 restraints weight = 356.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.038887 restraints weight = 232.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.039225 restraints weight = 166.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.039497 restraints weight = 125.972| |-----------------------------------------------------------------------------| r_work (final): 0.2390 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.052539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.052183 restraints weight = 514.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.052397 restraints weight = 99.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.052505 restraints weight = 33.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.052523 restraints weight = 12.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.052540 restraints weight = 4.687 | |-----------------------------------------------------------------------------| r_work (final): 0.2317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17997 Z= 0.195 Angle : 0.668 4.955 24459 Z= 0.364 Chirality : 0.041 0.156 2694 Planarity : 0.006 0.055 3132 Dihedral : 7.170 48.010 3075 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % 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: -3.25 (0.16), residues: 2172 helix: -0.15 (0.28), residues: 345 sheet: -2.51 (0.19), residues: 546 loop : -2.67 (0.14), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 575 TYR 0.019 0.002 TYR C 161 PHE 0.016 0.002 PHE E 213 TRP 0.014 0.002 TRP E 127 HIS 0.007 0.002 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (17943) covalent geometry : angle 0.65716 / 0.36 (24318) SS BOND : bond 0.01856 / 0.94 ( 21) SS BOND : angle 1.13046 / 0.66 ( 42) hydrogen bonds : bond 0.04456 / 2.98 ( 654) hydrogen bonds : angle 6.94962 / 4.81 ( 1845) link_BETA1-4 : bond 0.00492 / 0.25 ( 9) link_BETA1-4 : angle 1.73154 / 0.98 ( 27) link_NAG-ASN : bond 0.00844 / 0.51 ( 24) link_NAG-ASN : angle 1.95104 / 1.24 ( 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 33 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.147 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: C 38 GLU cc_start: 0.7611 (tp30) cc_final: 0.6578 (tt0) REVERT: C 208 HIS cc_start: 0.8609 (m90) cc_final: 0.8348 (m-70) REVERT: C 245 PHE cc_start: 0.9520 (m-80) cc_final: 0.9306 (m-80) outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.0620 time to fit residues: 3.0118 Evaluate side-chains 28 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.138 Evaluate side-chains 50 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.078 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: D 557 GLU cc_start: 0.9113 (pt0) cc_final: 0.8786 (pt0) REVERT: D 585 ASP cc_start: 0.9581 (m-30) cc_final: 0.9110 (p0) REVERT: D 590 ASP cc_start: 0.9450 (m-30) cc_final: 0.9203 (m-30) REVERT: D 592 TRP cc_start: 0.9261 (m100) cc_final: 0.8606 (m-10) REVERT: D 595 ASN cc_start: 0.9486 (m110) cc_final: 0.9168 (p0) REVERT: D 617 ASN cc_start: 0.9388 (m110) cc_final: 0.9137 (m110) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0884 time to fit residues: 5.1283 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 : 0.076 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 : 0.094 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 143 LEU cc_start: 0.9563 (tp) cc_final: 0.9229 (pp) REVERT: H 159 MET cc_start: 0.9101 (mmp) cc_final: 0.8736 (mmp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2759 time to fit residues: 9.5003 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 : 0.092 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: 0.0013 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: 0.0009 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: 3.9990 chunk 65 optimal weight: 2.9990 chunk 153 optimal weight: 0.0020 chunk 192 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 93 optimal weight: 0.0010 chunk 196 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 77 optimal weight: 0.0040 chunk 159 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 overall best weight: 0.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN H 164 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 = 0.3303 r_free = 0.3303 target = 0.056254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.044979 restraints weight = 47431.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.047932 restraints weight = 23015.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050198 restraints weight = 13389.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.051801 restraints weight = 8397.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.052989 restraints weight = 5536.218| |-----------------------------------------------------------------------------| r_work (final): 0.3210 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.075063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.062323 restraints weight = 28194.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.065665 restraints weight = 15936.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.068181 restraints weight = 9953.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.070018 restraints weight = 6474.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.071322 restraints weight = 4378.545| |-----------------------------------------------------------------------------| r_work (final): 0.3512 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.058165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.044607 restraints weight = 32917.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.048159 restraints weight = 17733.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.050772 restraints weight = 10788.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.052671 restraints weight = 6990.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.054000 restraints weight = 4785.955| |-----------------------------------------------------------------------------| r_work (final): 0.3482 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.041992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.039498 restraints weight = 599.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.040197 restraints weight = 281.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.040648 restraints weight = 170.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.040929 restraints weight = 119.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.041146 restraints weight = 90.231| |-----------------------------------------------------------------------------| r_work (final): 0.2420 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.052013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.051724 restraints weight = 452.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.051892 restraints weight = 89.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.051960 restraints weight = 30.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.051995 restraints weight = 11.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.051995 restraints weight = 4.290 | |-----------------------------------------------------------------------------| r_work (final): 0.2292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17997 Z= 0.130 Angle : 0.624 4.807 24459 Z= 0.336 Chirality : 0.043 0.178 2694 Planarity : 0.005 0.044 3132 Dihedral : 6.634 44.447 3075 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % 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: -2.94 (0.16), residues: 2172 helix: 0.17 (0.28), residues: 348 sheet: -2.27 (0.20), residues: 546 loop : -2.50 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 575 TYR 0.019 0.002 TYR G 33 PHE 0.015 0.002 PHE B 509 TRP 0.018 0.002 TRP H 36 HIS 0.014 0.001 HIS D 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (17943) covalent geometry : angle 0.61482 / 0.33 (24318) SS BOND : bond 0.01808 / 0.90 ( 21) SS BOND : angle 1.08276 / 0.63 ( 42) hydrogen bonds : bond 0.04126 / 2.76 ( 654) hydrogen bonds : angle 6.52690 / 4.51 ( 1845) link_BETA1-4 : bond 0.00553 / 0.30 ( 9) link_BETA1-4 : angle 1.55347 / 0.87 ( 27) link_NAG-ASN : bond 0.00809 / 0.49 ( 24) link_NAG-ASN : angle 1.68268 / 1.06 ( 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 38 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.136 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: C 38 GLU cc_start: 0.7436 (tp30) cc_final: 0.6371 (tt0) REVERT: C 245 PHE cc_start: 0.9506 (m-80) cc_final: 0.9259 (m-80) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.0594 time to fit residues: 3.3211 Evaluate side-chains 29 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.131 Evaluate side-chains 50 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.9525 (tp-100) cc_final: 0.9315 (tp-100) REVERT: B 582 LYS cc_start: 0.9214 (mmmt) cc_final: 0.9011 (mmmt) REVERT: B 585 ASP cc_start: 0.9316 (m-30) cc_final: 0.9105 (m-30) REVERT: B 590 ASP cc_start: 0.9548 (m-30) cc_final: 0.9271 (m-30) REVERT: B 592 TRP cc_start: 0.8535 (m100) cc_final: 0.7630 (t60) REVERT: B 595 ASN cc_start: 0.9177 (m110) cc_final: 0.8887 (p0) REVERT: B 611 HIS cc_start: 0.9225 (m-70) cc_final: 0.8928 (m170) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0960 time to fit residues: 5.4902 Evaluate side-chains 45 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.077 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 : 0.101 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: H 143 LEU cc_start: 0.9538 (tp) cc_final: 0.9086 (pp) REVERT: H 159 MET cc_start: 0.9012 (mmp) cc_final: 0.8583 (mmp) REVERT: H 204 TYR cc_start: 0.9178 (m-80) cc_final: 0.8564 (m-80) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2512 time to fit residues: 8.4391 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 : 0.084 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: 0.0016 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: 0.0011 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 ------------------------------------------------------------------------------- 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: 0.0470 chunk 115 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 163 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 186 optimal weight: 0.0980 chunk 209 optimal weight: 0.1980 chunk 112 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.055893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.044549 restraints weight = 47900.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.047576 restraints weight = 22960.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.049839 restraints weight = 13196.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.051419 restraints weight = 8243.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.052606 restraints weight = 5475.586| |-----------------------------------------------------------------------------| r_work (final): 0.3198 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.062667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.051378 restraints weight = 23381.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.054113 restraints weight = 12431.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.056092 restraints weight = 7583.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.057406 restraints weight = 4998.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.058639 restraints weight = 3559.230| |-----------------------------------------------------------------------------| r_work (final): 0.3428 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.059096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.043666 restraints weight = 30811.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.047718 restraints weight = 15406.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.050770 restraints weight = 8982.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.052932 restraints weight = 5682.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.054450 restraints weight = 3767.468| |-----------------------------------------------------------------------------| r_work (final): 0.3501 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.044344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.040896 restraints weight = 662.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.041534 restraints weight = 444.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.042051 restraints weight = 334.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.042470 restraints weight = 260.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.042672 restraints weight = 205.105| |-----------------------------------------------------------------------------| r_work (final): 0.2407 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.053611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.053478 restraints weight = 546.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.053572 restraints weight = 66.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.053604 restraints weight = 15.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.053607 restraints weight = 3.531 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.053607 restraints weight = 0.865 | |-----------------------------------------------------------------------------| r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17997 Z= 0.128 Angle : 0.620 7.265 24459 Z= 0.332 Chirality : 0.042 0.176 2694 Planarity : 0.005 0.042 3132 Dihedral : 6.407 41.084 3075 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % 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: -2.76 (0.16), residues: 2172 helix: 0.51 (0.29), residues: 348 sheet: -2.13 (0.20), residues: 540 loop : -2.47 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 316 TYR 0.020 0.002 TYR I 33 PHE 0.011 0.001 PHE G 192 TRP 0.015 0.001 TRP H 36 HIS 0.009 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17943) covalent geometry : angle 0.61106 / 0.33 (24318) SS BOND : bond 0.01810 / 0.91 ( 21) SS BOND : angle 1.02446 / 0.58 ( 42) hydrogen bonds : bond 0.04081 / 2.74 ( 654) hydrogen bonds : angle 6.40144 / 4.42 ( 1845) link_BETA1-4 : bond 0.00442 / 0.23 ( 9) link_BETA1-4 : angle 1.51355 / 0.85 ( 27) link_NAG-ASN : bond 0.00809 / 0.49 ( 24) link_NAG-ASN : angle 1.67814 / 1.06 ( 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 33 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.139 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: C 35 ASN cc_start: 0.9534 (m-40) cc_final: 0.8981 (t0) REVERT: C 38 GLU cc_start: 0.7334 (tp30) cc_final: 0.6472 (tt0) REVERT: C 245 PHE cc_start: 0.9496 (m-80) cc_final: 0.9261 (m-80) outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.0649 time to fit residues: 3.1239 Evaluate side-chains 25 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.137 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 : 0.077 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 557 GLU cc_start: 0.9103 (pt0) cc_final: 0.8775 (pt0) REVERT: D 585 ASP cc_start: 0.9704 (m-30) cc_final: 0.9222 (p0) REVERT: D 592 TRP cc_start: 0.9171 (m100) cc_final: 0.8624 (m-10) REVERT: D 595 ASN cc_start: 0.9464 (m110) cc_final: 0.9188 (p0) REVERT: D 617 ASN cc_start: 0.9410 (m110) cc_final: 0.9132 (m110) REVERT: D 620 GLU cc_start: 0.9813 (mm-30) cc_final: 0.9607 (mt-10) REVERT: D 646 ASP cc_start: 0.9355 (p0) cc_final: 0.9032 (m-30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0883 time to fit residues: 5.0158 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 : 0.074 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 : 0.093 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: symmetry clash revert: symmetry clash REVERT: H 143 LEU cc_start: 0.9357 (tp) cc_final: 0.8953 (pp) REVERT: H 159 MET cc_start: 0.9206 (mmp) cc_final: 0.8816 (mmp) REVERT: H 207 MET cc_start: 0.9019 (mtm) cc_final: 0.8769 (mtm) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2280 time to fit residues: 7.7033 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 : 0.093 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: 0.0870 chunk 134 optimal weight: 7.9990 chunk 146 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 163 optimal weight: 0.0370 chunk 79 optimal weight: 6.9990 chunk 152 optimal weight: 0.0870 chunk 100 optimal weight: 2.9990 chunk 147 optimal weight: 0.0050 overall best weight: 0.0628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.056974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.045792 restraints weight = 46857.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.048855 restraints weight = 22085.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.051106 restraints weight = 12525.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.052708 restraints weight = 7770.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.053832 restraints weight = 5091.597| |-----------------------------------------------------------------------------| r_work (final): 0.3227 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.109000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.097734 restraints weight = 31851.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.099987 restraints weight = 14777.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.101257 restraints weight = 7807.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.102050 restraints weight = 4557.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.102569 restraints weight = 2767.718| |-----------------------------------------------------------------------------| r_work (final): 0.3461 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.058839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.042720 restraints weight = 28346.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.046698 restraints weight = 14294.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.049725 restraints weight = 8421.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.051892 restraints weight = 5411.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.053418 restraints weight = 3669.345| |-----------------------------------------------------------------------------| r_work (final): 0.3549 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.045002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.042674 restraints weight = 552.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.043165 restraints weight = 309.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.043511 restraints weight = 218.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.043836 restraints weight = 164.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.043837 restraints weight = 130.271| |-----------------------------------------------------------------------------| r_work (final): 0.2455 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.054480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.054330 restraints weight = 432.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.054422 restraints weight = 57.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.054441 restraints weight = 9.965 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.054432 restraints weight = 2.312 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.054432 restraints weight = 0.148 | |-----------------------------------------------------------------------------| r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.6887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17997 Z= 0.128 Angle : 0.615 6.396 24459 Z= 0.332 Chirality : 0.043 0.179 2694 Planarity : 0.005 0.043 3132 Dihedral : 6.282 39.550 3075 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % 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 : 0.14 % 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: -2.64 (0.17), residues: 2172 helix: 0.67 (0.29), residues: 348 sheet: -2.07 (0.19), residues: 576 loop : -2.38 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 575 TYR 0.020 0.001 TYR G 33 PHE 0.026 0.002 PHE C 115 TRP 0.045 0.002 TRP E 80 HIS 0.008 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (17943) covalent geometry : angle 0.60705 / 0.33 (24318) SS BOND : bond 0.01804 / 0.90 ( 21) SS BOND : angle 0.99866 / 0.57 ( 42) hydrogen bonds : bond 0.03989 / 2.68 ( 654) hydrogen bonds : angle 6.27383 / 4.33 ( 1845) link_BETA1-4 : bond 0.00442 / 0.23 ( 9) link_BETA1-4 : angle 1.48151 / 0.83 ( 27) link_NAG-ASN : bond 0.00815 / 0.50 ( 24) link_NAG-ASN : angle 1.61357 / 1.02 ( 72) =============================================================================== Job complete usr+sys time: 2670.80 seconds wall clock time: 47 minutes 12.05 seconds (2832.05 seconds total)