Starting phenix.real_space_refine on Mon Sep 14 23:02:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5uk2_8564/09_2026/5uk2_8564_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5uk2_8564/09_2026/5uk2_8564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5uk2_8564/09_2026/5uk2_8564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5uk2_8564/09_2026/5uk2_8564.map" model { file = "/net/cci-nas-00/data/ceres_data/5uk2_8564/09_2026/5uk2_8564_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5uk2_8564/09_2026/5uk2_8564_trim.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.071 sd= 0.458 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 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33948 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "B" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "C" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "D" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "E" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "F" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "G" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "H" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "I" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.39, per 1000 atoms: 0.16 Number of scatterers: 33948 At special positions: 0 Unit cell: (142.68, 131.2, 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=2.06 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 637 " distance=2.06 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 637 " distance=1.95 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=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.02 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=2.02 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: 3.19 Conformation dependent library (CDL) restraints added in 762.8 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, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 removed outlier: 3.879A 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: 4.221A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 4.158A 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: 3.579A pdb=" N GLN B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 626 " --> pdb=" O VAL B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 654 Processing helix chain 'B' and resid 662 through 670 Processing helix chain 'C' and resid 60 through 67 removed outlier: 3.879A 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: 4.221A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 4.158A 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: 3.579A pdb=" N GLN D 625 " --> pdb=" O LYS D 621 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 626 " --> pdb=" O VAL D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 654 Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'E' and resid 60 through 67 removed outlier: 3.880A 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: 4.220A pdb=" N TRP E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 4.159A 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: 3.579A pdb=" N GLN F 625 " --> pdb=" O LYS F 621 " (cutoff:3.500A) removed outlier: 3.690A 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: 3.535A 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: 3.535A 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: 4.125A pdb=" N CYS B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 22 removed outlier: 4.233A pdb=" N ASP A 18 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 22 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 48 removed outlier: 5.855A pdb=" N LEU A 45 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS A 278 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.798A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 118 removed outlier: 8.380A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 118 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 140 removed outlier: 4.584A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.904A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 531 through 536 removed outlier: 4.125A pdb=" N CYS D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 18 through 22 removed outlier: 4.234A pdb=" N ASP C 18 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR C 22 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 48 removed outlier: 5.855A pdb=" N LEU C 45 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS C 278 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.798A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 118 removed outlier: 8.381A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 115 through 118 Processing sheet with id=AB9, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.584A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC2, first strand: chain 'C' and resid 287 through 289 removed outlier: 3.903A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 531 through 536 removed outlier: 4.125A pdb=" N CYS F 637 " --> pdb=" O ILE F 633 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 18 through 22 removed outlier: 4.234A pdb=" N ASP E 18 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR E 22 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 48 removed outlier: 5.855A pdb=" N LEU E 45 " --> pdb=" O ASP E 276 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N CYS E 278 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.798A pdb=" N LEU E 54 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 115 through 118 removed outlier: 8.381A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 115 through 118 Processing sheet with id=AD1, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.584A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'E' and resid 287 through 289 removed outlier: 3.903A pdb=" N CYS E 282 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 13 removed outlier: 7.036A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'G' and resid 129 through 132 Processing sheet with id=AD8, first strand: chain 'G' and resid 136 through 137 removed outlier: 6.976A pdb=" N MET G 159 " --> pdb=" O GLY G 175 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY G 175 " --> pdb=" O MET G 159 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TRP G 161 " --> pdb=" O VAL G 173 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL G 173 " --> pdb=" O TRP G 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 136 through 137 Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 13 removed outlier: 7.036A pdb=" N LEU H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE4, first strand: chain 'H' and resid 129 through 132 Processing sheet with id=AE5, first strand: chain 'H' and resid 136 through 137 removed outlier: 6.976A pdb=" N MET H 159 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY H 175 " --> pdb=" O MET H 159 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TRP H 161 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL H 173 " --> pdb=" O TRP H 161 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 136 through 137 Processing sheet with id=AE7, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 13 removed outlier: 7.036A pdb=" N LEU I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AF1, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AF2, first strand: chain 'I' and resid 136 through 137 removed outlier: 6.977A pdb=" N MET I 159 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLY I 175 " --> pdb=" O MET I 159 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TRP I 161 " --> pdb=" O VAL I 173 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL I 173 " --> pdb=" O TRP I 161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 136 through 137 738 hydrogen bonds defined for protein. 1962 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: 9.25 Time building geometry restraints manager: 4.37 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: 7672 1.42 - 1.62: 10169 1.62 - 1.82: 102 Bond restraints: 34344 Sorted by residual: bond pdb=" CA GLN H 90 " pdb=" CB GLN H 90 " ideal model delta sigma weight residual 1.530 1.483 0.048 1.50e-02 4.44e+03 1.01e+01 bond pdb=" CA GLN G 90 " pdb=" CB GLN G 90 " ideal model delta sigma weight residual 1.530 1.483 0.048 1.50e-02 4.44e+03 1.00e+01 bond pdb=" CA GLN I 90 " pdb=" CB GLN I 90 " ideal model delta sigma weight residual 1.530 1.483 0.047 1.50e-02 4.44e+03 9.99e+00 bond pdb=" CB GLN G 91 " pdb=" CG GLN G 91 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.53e+00 bond pdb=" CB GLN H 91 " pdb=" CG GLN H 91 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.53e+00 ... (remaining 34339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 54580 2.05 - 4.09: 5991 4.09 - 6.14: 823 6.14 - 8.18: 137 8.18 - 10.23: 26 Bond angle restraints: 61557 Sorted by residual: angle pdb=" N GLY G 31 " pdb=" CA GLY G 31 " pdb=" C GLY G 31 " ideal model delta sigma weight residual 115.36 124.62 -9.26 1.33e+00 5.65e-01 4.85e+01 angle pdb=" N GLY H 31 " pdb=" CA GLY H 31 " pdb=" C GLY H 31 " ideal model delta sigma weight residual 115.36 124.60 -9.24 1.33e+00 5.65e-01 4.83e+01 angle pdb=" N GLY I 31 " pdb=" CA GLY I 31 " pdb=" C GLY I 31 " ideal model delta sigma weight residual 115.36 124.59 -9.23 1.33e+00 5.65e-01 4.82e+01 angle pdb=" N SER G 30 " pdb=" CA SER G 30 " pdb=" C SER G 30 " ideal model delta sigma weight residual 113.28 122.30 -9.02 1.57e+00 4.06e-01 3.30e+01 angle pdb=" N SER I 30 " pdb=" CA SER I 30 " pdb=" C SER I 30 " ideal model delta sigma weight residual 113.28 122.29 -9.01 1.57e+00 4.06e-01 3.29e+01 ... (remaining 61552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.70: 15423 19.70 - 39.39: 1065 39.39 - 59.09: 259 59.09 - 78.79: 35 78.79 - 98.48: 24 Dihedral angle restraints: 16806 sinusoidal: 9345 harmonic: 7461 Sorted by residual: dihedral pdb=" CA ILE H 94 " pdb=" C ILE H 94 " pdb=" N SER H 95 " pdb=" CA SER H 95 " ideal model delta harmonic sigma weight residual 180.00 146.12 33.88 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA ILE G 94 " pdb=" C ILE G 94 " pdb=" N SER G 95 " pdb=" CA SER G 95 " ideal model delta harmonic sigma weight residual 180.00 146.13 33.87 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA ILE I 94 " pdb=" C ILE I 94 " pdb=" N SER I 95 " pdb=" CA SER I 95 " ideal model delta harmonic sigma weight residual 180.00 146.14 33.86 0 5.00e+00 4.00e-02 4.59e+01 ... (remaining 16803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2203 0.083 - 0.167: 425 0.167 - 0.250: 57 0.250 - 0.333: 6 0.333 - 0.416: 3 Chirality restraints: 2694 Sorted by residual: 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 -2.21 -0.19 2.00e-02 2.50e+03 9.10e+01 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 -2.21 -0.19 2.00e-02 2.50e+03 8.75e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.58e+01 ... (remaining 2691 not shown) Planarity restraints: 5244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 248 " 0.190 2.00e-02 2.50e+03 2.31e-01 7.97e+02 pdb=" CG ASN C 248 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN C 248 " -0.201 2.00e-02 2.50e+03 pdb=" ND2 ASN C 248 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 248 " -0.348 2.00e-02 2.50e+03 pdb="HD22 ASN C 248 " 0.349 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 248 " -0.189 2.00e-02 2.50e+03 2.29e-01 7.90e+02 pdb=" CG ASN E 248 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN E 248 " 0.200 2.00e-02 2.50e+03 pdb=" ND2 ASN E 248 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN E 248 " 0.346 2.00e-02 2.50e+03 pdb="HD22 ASN E 248 " -0.347 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 248 " -0.187 2.00e-02 2.50e+03 2.27e-01 7.73e+02 pdb=" CG ASN A 248 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN A 248 " 0.199 2.00e-02 2.50e+03 pdb=" ND2 ASN A 248 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 248 " 0.342 2.00e-02 2.50e+03 pdb="HD22 ASN A 248 " -0.343 2.00e-02 2.50e+03 ... (remaining 5241 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 7469 2.30 - 2.88: 76943 2.88 - 3.45: 85336 3.45 - 4.03: 117596 4.03 - 4.60: 175538 Nonbonded interactions: 462882 Sorted by model distance: nonbonded pdb=" HE2 HIS E 130 " pdb=" O PRO E 162 " model vdw 1.727 2.450 nonbonded pdb=" HE2 HIS A 130 " pdb=" O PRO A 162 " model vdw 1.728 2.450 nonbonded pdb=" HE2 HIS C 130 " pdb=" O PRO C 162 " model vdw 1.728 2.450 nonbonded pdb=" H GLY I 140 " pdb=" O LEU I 210 " model vdw 1.736 2.450 nonbonded pdb=" H GLY G 140 " pdb=" O LEU G 210 " model vdw 1.736 2.450 ... (remaining 462877 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: 0.090 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: 0.240 Extract box with map and model: 0.440 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.230 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.012 0.130 17997 Z= 0.520 Angle : 1.378 10.225 24459 Z= 0.787 Chirality : 0.067 0.416 2694 Planarity : 0.009 0.082 3132 Dihedral : 12.486 98.484 7023 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.75 % Favored : 91.11 % Rotamer: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 1.00 % 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: -4.11 (0.14), residues: 2172 helix: -1.67 (0.22), residues: 333 sheet: -2.66 (0.17), residues: 585 loop : -3.17 (0.14), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG I 222 TYR 0.029 0.005 TYR G 236 PHE 0.042 0.005 PHE E 147 TRP 0.032 0.006 TRP C 153 HIS 0.019 0.004 HIS F 611 Details of bonding type rmsd/Z covalent geometry : bond 0.01174 / 0.52 (17943) covalent geometry : angle 1.35522 / 0.78 (24318) SS BOND : bond 0.02096 / 1.41 ( 21) SS BOND : angle 2.52248 / 1.43 ( 42) hydrogen bonds : bond 0.11098 / 7.32 ( 678) hydrogen bonds : angle 10.59038 / 7.43 ( 1962) link_BETA1-4 : bond 0.01433 / 0.73 ( 9) link_BETA1-4 : angle 4.31921 / 2.63 ( 27) link_NAG-ASN : bond 0.01320 / 0.80 ( 24) link_NAG-ASN : angle 3.77841 / 2.33 ( 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 98 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 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: A 12 HIS cc_start: 0.7741 (t70) cc_final: 0.6858 (m90) REVERT: A 38 GLU cc_start: 0.8519 (tp30) cc_final: 0.7871 (tm-30) REVERT: A 39 ASP cc_start: 0.9326 (p0) cc_final: 0.9080 (p0) REVERT: A 70 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7627 (pt0) REVERT: A 87 PRO cc_start: 0.8179 (Cg_exo) cc_final: 0.7958 (Cg_endo) REVERT: A 104 GLU cc_start: 0.6193 (mm-30) cc_final: 0.5827 (tp30) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.1473 time to fit residues: 16.8400 Evaluate side-chains 48 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.135 Evaluate side-chains 67 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 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: B 578 GLU cc_start: 0.8124 (tt0) cc_final: 0.7832 (tm-30) REVERT: B 605 GLU cc_start: 0.8896 (tp30) cc_final: 0.8620 (tm-30) REVERT: B 610 PHE cc_start: 0.8140 (t80) cc_final: 0.7867 (t80) REVERT: B 618 LEU cc_start: 0.9063 (tp) cc_final: 0.8685 (tp) REVERT: B 619 TYR cc_start: 0.8536 (t80) cc_final: 0.8163 (t80) REVERT: B 622 VAL cc_start: 0.8871 (t) cc_final: 0.8426 (m) REVERT: B 633 ILE cc_start: 0.8025 (pt) cc_final: 0.7443 (tp) REVERT: B 640 PHE cc_start: 0.8296 (m-10) cc_final: 0.7885 (m-10) REVERT: B 670 ARG cc_start: 0.7686 (ttp-110) cc_final: 0.7369 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1348 time to fit residues: 9.9043 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 : 0.071 Evaluate side-chains 52 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.086 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: G 17 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6572 (mm-30) REVERT: G 48 LEU cc_start: 0.7088 (mt) cc_final: 0.6628 (mt) REVERT: G 160 HIS cc_start: 0.8383 (m-70) cc_final: 0.7960 (m-70) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1703 time to fit residues: 9.8057 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 : 0.095 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 : 0.001 ------------------------------------------------------------------------------- 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: 7.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS A 191 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 = 0.3596 r_free = 0.3596 target = 0.108174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094753 restraints weight = 22458.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098880 restraints weight = 11239.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.101700 restraints weight = 6504.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.103464 restraints weight = 4052.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.104697 restraints weight = 2690.724| |-----------------------------------------------------------------------------| r_work (final): 0.3527 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.111479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098328 restraints weight = 12198.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.101673 restraints weight = 6331.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.103882 restraints weight = 3748.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.105390 restraints weight = 2435.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.106455 restraints weight = 1709.832| |-----------------------------------------------------------------------------| r_work (final): 0.3734 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.097241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.088699 restraints weight = 20912.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.091859 restraints weight = 10240.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.093855 restraints weight = 5621.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.095067 restraints weight = 3262.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.095756 restraints weight = 1977.633| |-----------------------------------------------------------------------------| r_work (final): 0.3846 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.068018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.067920 restraints weight = 383.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.067993 restraints weight = 39.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.068009 restraints weight = 8.530 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.068018 restraints weight = 2.000 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.068017 restraints weight = 0.436 | |-----------------------------------------------------------------------------| r_work (final): 0.2808 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.075803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.075130 restraints weight = 238.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.075458 restraints weight = 75.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.075600 restraints weight = 23.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.075600 restraints weight = 11.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.075600 restraints weight = 11.655| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 17997 Z= 0.305 Angle : 0.928 10.564 24459 Z= 0.505 Chirality : 0.048 0.212 2694 Planarity : 0.007 0.059 3132 Dihedral : 10.877 60.686 3075 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.49 % Allowed : 1.29 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -3.68 (0.15), residues: 2172 helix: -0.57 (0.26), residues: 330 sheet: -2.74 (0.17), residues: 567 loop : -2.92 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 576 TYR 0.050 0.003 TYR H 33 PHE 0.028 0.003 PHE D 570 TRP 0.010 0.002 TRP A 127 HIS 0.006 0.002 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.30 (17943) covalent geometry : angle 0.90764 / 0.50 (24318) SS BOND : bond 0.03521 / 1.99 ( 21) SS BOND : angle 2.70112 / 1.67 ( 42) hydrogen bonds : bond 0.05672 / 3.73 ( 678) hydrogen bonds : angle 8.27986 / 5.81 ( 1962) link_BETA1-4 : bond 0.00543 / 0.27 ( 9) link_BETA1-4 : angle 2.13211 / 1.22 ( 27) link_NAG-ASN : bond 0.00882 / 0.51 ( 24) link_NAG-ASN : angle 2.91870 / 1.79 ( 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 68 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.138 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: A 12 HIS cc_start: 0.7702 (t70) cc_final: 0.6667 (m90) REVERT: A 38 GLU cc_start: 0.8326 (tp30) cc_final: 0.7888 (tm-30) REVERT: A 70 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7675 (pt0) REVERT: A 87 PRO cc_start: 0.8460 (Cg_exo) cc_final: 0.8140 (Cg_endo) REVERT: A 104 GLU cc_start: 0.6556 (mm-30) cc_final: 0.6207 (tp30) outliers start: 3 outliers final: 1 residues processed: 66 average time/residue: 0.0973 time to fit residues: 8.1590 Evaluate side-chains 47 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.170 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 : 0.100 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: B 541 THR cc_start: 0.9103 (m) cc_final: 0.8872 (m) REVERT: B 578 GLU cc_start: 0.8002 (tt0) cc_final: 0.7746 (tp30) REVERT: B 590 ASP cc_start: 0.8617 (m-30) cc_final: 0.8343 (m-30) REVERT: B 602 LEU cc_start: 0.9123 (mm) cc_final: 0.8921 (mm) REVERT: B 620 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8916 (tp30) REVERT: B 622 VAL cc_start: 0.8796 (t) cc_final: 0.8581 (t) REVERT: B 649 MET cc_start: 0.8699 (mmt) cc_final: 0.8113 (mpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1191 time to fit residues: 6.9206 Evaluate side-chains 34 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.093 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 : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 17 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6555 (mm-30) REVERT: H 48 LEU cc_start: 0.6664 (mt) cc_final: 0.6200 (mt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1129 time to fit residues: 5.2094 Evaluate side-chains 27 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.117 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: 0.0017 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 150 optimal weight: 0.2980 chunk 30 optimal weight: 0.0870 chunk 16 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 86 optimal weight: 0.4980 chunk 176 optimal weight: 6.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.109991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094858 restraints weight = 21942.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.099169 restraints weight = 11027.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.102087 restraints weight = 6439.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104047 restraints weight = 4111.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.105371 restraints weight = 2811.563| |-----------------------------------------------------------------------------| r_work (final): 0.3535 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.119087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.104202 restraints weight = 11949.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.108447 restraints weight = 6193.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.111147 restraints weight = 3599.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.112924 restraints weight = 2309.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.114224 restraints weight = 1583.668| |-----------------------------------------------------------------------------| r_work (final): 0.3813 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.097733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.088240 restraints weight = 21164.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.091699 restraints weight = 10483.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.093881 restraints weight = 5680.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.095136 restraints weight = 3287.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.095758 restraints weight = 2054.112| |-----------------------------------------------------------------------------| r_work (final): 0.3847 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.072028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.071875 restraints weight = 405.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.071969 restraints weight = 49.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.071992 restraints weight = 11.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.071996 restraints weight = 3.176 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.071996 restraints weight = 2.459 | |-----------------------------------------------------------------------------| r_work (final): 0.2893 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.103171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.100007 restraints weight = 173.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.100328 restraints weight = 134.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.100527 restraints weight = 102.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.100527 restraints weight = 79.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.100527 restraints weight = 79.453| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 17997 Z= 0.221 Angle : 0.823 13.285 24459 Z= 0.448 Chirality : 0.046 0.192 2694 Planarity : 0.006 0.060 3132 Dihedral : 9.128 46.122 3075 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.16 % Allowed : 2.59 % Favored : 97.25 % 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: -3.35 (0.16), residues: 2172 helix: -0.78 (0.26), residues: 348 sheet: -2.31 (0.19), residues: 546 loop : -2.70 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 575 TYR 0.053 0.002 TYR I 33 PHE 0.018 0.002 PHE B 509 TRP 0.008 0.001 TRP A 127 HIS 0.008 0.002 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (17943) covalent geometry : angle 0.80363 / 0.44 (24318) SS BOND : bond 0.02980 / 1.80 ( 21) SS BOND : angle 2.10652 / 1.39 ( 42) hydrogen bonds : bond 0.05629 / 3.78 ( 678) hydrogen bonds : angle 7.69550 / 5.41 ( 1962) link_BETA1-4 : bond 0.00601 / 0.36 ( 9) link_BETA1-4 : angle 2.03998 / 1.15 ( 27) link_NAG-ASN : bond 0.00805 / 0.49 ( 24) link_NAG-ASN : angle 2.78707 / 1.72 ( 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 65 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 HIS cc_start: 0.6714 (t70) cc_final: 0.6110 (m90) REVERT: C 37 LEU cc_start: 0.7800 (tp) cc_final: 0.6892 (tp) REVERT: C 56 LEU cc_start: 0.9511 (mp) cc_final: 0.8860 (mt) REVERT: C 59 CYS cc_start: 0.7976 (m) cc_final: 0.7417 (t) REVERT: C 70 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7659 (pt0) REVERT: C 83 ILE cc_start: 0.8951 (mt) cc_final: 0.8504 (mt) REVERT: C 87 PRO cc_start: 0.8315 (Cg_exo) cc_final: 0.8046 (Cg_endo) REVERT: C 98 HIS cc_start: 0.7971 (t70) cc_final: 0.7683 (t70) REVERT: C 102 TYR cc_start: 0.7443 (t80) cc_final: 0.7216 (t80) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.0659 time to fit residues: 5.8986 Evaluate side-chains 46 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.137 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 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: B 541 THR cc_start: 0.9147 (m) cc_final: 0.8899 (m) REVERT: B 590 ASP cc_start: 0.8575 (m-30) cc_final: 0.8343 (m-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1032 time to fit residues: 4.9128 Evaluate side-chains 31 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.067 Evaluate side-chains 35 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 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: H 17 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6313 (mm-30) REVERT: H 48 LEU cc_start: 0.6601 (mt) cc_final: 0.6029 (mt) REVERT: H 87 TYR cc_start: 0.5326 (m-80) cc_final: 0.4765 (m-80) REVERT: H 138 GLN cc_start: 0.6672 (pm20) cc_final: 0.6290 (mp10) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0747 time to fit residues: 3.2808 Evaluate side-chains 23 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.090 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 : 0.001 ------------------------------------------------------------------------------- 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: 1.9990 chunk 40 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 24 optimal weight: 0.0060 chunk 29 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 73 optimal weight: 0.0170 chunk 136 optimal weight: 0.0020 chunk 150 optimal weight: 0.1980 chunk 176 optimal weight: 4.9990 overall best weight: 0.2444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS 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 = 0.3633 r_free = 0.3633 target = 0.110392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096176 restraints weight = 22037.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.100274 restraints weight = 10865.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.103111 restraints weight = 6252.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.104949 restraints weight = 3935.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106213 restraints weight = 2671.756| |-----------------------------------------------------------------------------| r_work (final): 0.3562 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.115210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.101668 restraints weight = 11772.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.105481 restraints weight = 6216.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.107899 restraints weight = 3626.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.109446 restraints weight = 2309.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.110620 restraints weight = 1593.865| |-----------------------------------------------------------------------------| r_work (final): 0.3800 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.100067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.090712 restraints weight = 22458.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.093928 restraints weight = 11597.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.095923 restraints weight = 6609.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.097245 restraints weight = 4044.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.097974 restraints weight = 2634.816| |-----------------------------------------------------------------------------| r_work (final): 0.3868 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.078458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.078195 restraints weight = 308.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.078407 restraints weight = 56.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.078443 restraints weight = 13.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.078445 restraints weight = 3.838 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.078445 restraints weight = 1.056 | |-----------------------------------------------------------------------------| r_work (final): 0.2963 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.073741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.073251 restraints weight = 147.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.073530 restraints weight = 62.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.073622 restraints weight = 27.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.073683 restraints weight = 12.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.073713 restraints weight = 6.005 | |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17997 Z= 0.139 Angle : 0.703 6.551 24459 Z= 0.376 Chirality : 0.044 0.195 2694 Planarity : 0.006 0.098 3132 Dihedral : 7.869 40.034 3075 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.16), residues: 2172 helix: -0.18 (0.26), residues: 351 sheet: -2.00 (0.20), residues: 546 loop : -2.63 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 117 TYR 0.037 0.002 TYR I 33 PHE 0.015 0.002 PHE F 610 TRP 0.005 0.001 TRP E 234 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (17943) covalent geometry : angle 0.68577 / 0.37 (24318) SS BOND : bond 0.02040 / 1.25 ( 21) SS BOND : angle 1.94685 / 1.24 ( 42) hydrogen bonds : bond 0.04885 / 3.28 ( 678) hydrogen bonds : angle 7.11177 / 5.00 ( 1962) link_BETA1-4 : bond 0.00381 / 0.23 ( 9) link_BETA1-4 : angle 1.59703 / 0.91 ( 27) link_NAG-ASN : bond 0.00760 / 0.48 ( 24) link_NAG-ASN : angle 2.42866 / 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 63 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.152 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: C 12 HIS cc_start: 0.6685 (t70) cc_final: 0.6375 (m90) REVERT: C 56 LEU cc_start: 0.9390 (mp) cc_final: 0.9129 (mt) REVERT: C 70 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7794 (pt0) REVERT: C 83 ILE cc_start: 0.8890 (mt) cc_final: 0.8662 (mt) REVERT: C 98 HIS cc_start: 0.8086 (t70) cc_final: 0.7769 (t70) REVERT: C 256 TYR cc_start: 0.8345 (m-80) cc_final: 0.7910 (m-80) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.0646 time to fit residues: 5.7447 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 : 0.143 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 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: B 541 THR cc_start: 0.9181 (m) cc_final: 0.8955 (m) REVERT: B 589 ILE cc_start: 0.8016 (mt) cc_final: 0.7454 (tp) REVERT: B 590 ASP cc_start: 0.8392 (m-30) cc_final: 0.8143 (m-30) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1124 time to fit residues: 5.5834 Evaluate side-chains 33 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.078 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 : 0.097 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: G 17 GLU cc_start: 0.6435 (mm-30) cc_final: 0.6142 (mm-30) REVERT: G 87 TYR cc_start: 0.5355 (m-80) cc_final: 0.5119 (m-80) REVERT: G 131 GLU cc_start: 0.7677 (mp0) cc_final: 0.7368 (mp0) REVERT: G 138 GLN cc_start: 0.6801 (pm20) cc_final: 0.6556 (mp10) REVERT: G 171 GLU cc_start: 0.6742 (tt0) cc_final: 0.6358 (mp0) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0783 time to fit residues: 3.5459 Evaluate side-chains 22 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.110 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: 0.0011 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 156 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 134 optimal weight: 0.7980 chunk 193 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 164 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 = 0.3616 r_free = 0.3616 target = 0.109021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.094300 restraints weight = 21571.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.098505 restraints weight = 10731.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.101342 restraints weight = 6217.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.103210 restraints weight = 3950.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.104546 restraints weight = 2723.189| |-----------------------------------------------------------------------------| r_work (final): 0.3540 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.114172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.100323 restraints weight = 11793.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104209 restraints weight = 6286.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.106680 restraints weight = 3722.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.108245 restraints weight = 2390.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.109285 restraints weight = 1649.737| |-----------------------------------------------------------------------------| r_work (final): 0.3776 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.098083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.090165 restraints weight = 22052.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.092930 restraints weight = 11111.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.094649 restraints weight = 6284.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.095697 restraints weight = 3850.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.096390 restraints weight = 2496.943| |-----------------------------------------------------------------------------| r_work (final): 0.3864 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.079180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.078774 restraints weight = 368.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.079040 restraints weight = 71.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.079096 restraints weight = 19.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.079125 restraints weight = 5.480 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.079125 restraints weight = 2.307 | |-----------------------------------------------------------------------------| r_work (final): 0.2972 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.077397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.077262 restraints weight = 259.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.077293 restraints weight = 18.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.077299 restraints weight = 1.446 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.077296 restraints weight = 0.115 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.077268 restraints weight = 289.039| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.5394 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= 0.186 Angle : 0.685 7.433 24459 Z= 0.366 Chirality : 0.042 0.171 2694 Planarity : 0.005 0.043 3132 Dihedral : 7.440 33.767 3075 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % 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 : 0.14 % 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: -2.96 (0.16), residues: 2172 helix: -0.11 (0.27), residues: 357 sheet: -1.97 (0.20), residues: 531 loop : -2.62 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 575 TYR 0.023 0.002 TYR A 161 PHE 0.013 0.002 PHE G 84 TRP 0.006 0.001 TRP E 80 HIS 0.004 0.001 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (17943) covalent geometry : angle 0.66850 / 0.36 (24318) SS BOND : bond 0.01992 / 1.23 ( 21) SS BOND : angle 1.75596 / 1.11 ( 42) hydrogen bonds : bond 0.04930 / 3.32 ( 678) hydrogen bonds : angle 6.89155 / 4.84 ( 1962) link_BETA1-4 : bond 0.00330 / 0.19 ( 9) link_BETA1-4 : angle 1.49900 / 0.88 ( 27) link_NAG-ASN : bond 0.00787 / 0.48 ( 24) link_NAG-ASN : angle 2.38187 / 1.48 ( 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 58 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 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: C 70 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7562 (pt0) REVERT: C 83 ILE cc_start: 0.8760 (mt) cc_final: 0.8492 (mt) REVERT: C 107 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7988 (tt0) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.0571 time to fit residues: 4.6436 Evaluate side-chains 45 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.083 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 : 0.046 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: B 589 ILE cc_start: 0.8068 (mt) cc_final: 0.7601 (tp) REVERT: B 590 ASP cc_start: 0.8397 (m-30) cc_final: 0.8160 (m-30) REVERT: B 619 TYR cc_start: 0.7934 (t80) cc_final: 0.7563 (t80) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0846 time to fit residues: 4.1735 Evaluate side-chains 33 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.071 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 : 0.095 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: G 17 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6236 (mm-30) REVERT: G 131 GLU cc_start: 0.7721 (mp0) cc_final: 0.7348 (mp0) REVERT: G 138 GLN cc_start: 0.7154 (pm20) cc_final: 0.6749 (mp10) REVERT: G 171 GLU cc_start: 0.6940 (tt0) cc_final: 0.6609 (mp0) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0804 time to fit residues: 3.0339 Evaluate side-chains 22 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.055 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0008 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 4 optimal weight: 0.3980 chunk 151 optimal weight: 0.3980 chunk 114 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 196 optimal weight: 0.0570 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 0.0010 chunk 159 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 overall best weight: 0.9706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.110115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095416 restraints weight = 21205.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.099767 restraints weight = 10332.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102645 restraints weight = 5887.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.104637 restraints weight = 3705.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.105887 restraints weight = 2477.550| |-----------------------------------------------------------------------------| r_work (final): 0.3561 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.116019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.101997 restraints weight = 12066.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105976 restraints weight = 6441.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.108508 restraints weight = 3814.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.110184 restraints weight = 2458.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.111279 restraints weight = 1682.015| |-----------------------------------------------------------------------------| r_work (final): 0.3799 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.098076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.090616 restraints weight = 23301.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.093302 restraints weight = 11768.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.094889 restraints weight = 6590.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.095920 restraints weight = 4044.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.096340 restraints weight = 2603.744| |-----------------------------------------------------------------------------| r_work (final): 0.3868 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.081975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.081367 restraints weight = 363.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.081772 restraints weight = 90.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.081895 restraints weight = 28.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.081937 restraints weight = 9.870 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.081952 restraints weight = 3.509 | |-----------------------------------------------------------------------------| r_work (final): 0.3012 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.071870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.071806 restraints weight = 231.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.071809 restraints weight = 13.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.071802 restraints weight = 0.883 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.071802 restraints weight = 0.058 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 5)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.071802 restraints weight = 0.040 | |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 17997 Z= 0.181 Angle : 0.679 11.002 24459 Z= 0.361 Chirality : 0.043 0.180 2694 Planarity : 0.006 0.074 3132 Dihedral : 7.013 31.261 3075 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.16), residues: 2172 helix: 0.08 (0.26), residues: 357 sheet: -1.81 (0.21), residues: 534 loop : -2.64 (0.15), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 575 TYR 0.019 0.001 TYR E 161 PHE 0.014 0.001 PHE F 509 TRP 0.005 0.001 TRP E 234 HIS 0.006 0.001 HIS I 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (17943) covalent geometry : angle 0.66413 / 0.36 (24318) SS BOND : bond 0.02088 / 1.30 ( 21) SS BOND : angle 1.92569 / 1.14 ( 42) hydrogen bonds : bond 0.05057 / 3.40 ( 678) hydrogen bonds : angle 6.70878 / 4.72 ( 1962) link_BETA1-4 : bond 0.00382 / 0.23 ( 9) link_BETA1-4 : angle 1.42674 / 0.82 ( 27) link_NAG-ASN : bond 0.00754 / 0.47 ( 24) link_NAG-ASN : angle 2.15816 / 1.33 ( 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 60 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 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: C 70 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7646 (pt0) REVERT: C 83 ILE cc_start: 0.8713 (mt) cc_final: 0.8408 (mt) REVERT: C 105 LEU cc_start: 0.9458 (tp) cc_final: 0.9258 (tp) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.0654 time to fit residues: 5.4913 Evaluate side-chains 45 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.131 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 : 0.073 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: B 577 MET cc_start: 0.8336 (mmt) cc_final: 0.7857 (mmt) REVERT: B 589 ILE cc_start: 0.8182 (mt) cc_final: 0.7396 (tp) REVERT: B 590 ASP cc_start: 0.8482 (m-30) cc_final: 0.8196 (m-30) REVERT: B 619 TYR cc_start: 0.7875 (t80) cc_final: 0.7341 (t80) REVERT: B 620 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8909 (mm-30) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0708 time to fit residues: 3.7244 Evaluate side-chains 34 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.075 Evaluate side-chains 31 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.090 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: G 17 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6385 (mm-30) REVERT: G 131 GLU cc_start: 0.7777 (mp0) cc_final: 0.7332 (mp0) REVERT: G 138 GLN cc_start: 0.7140 (pm20) cc_final: 0.6774 (mp10) REVERT: G 160 HIS cc_start: 0.8427 (m-70) cc_final: 0.8053 (m-70) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0734 time to fit residues: 2.8228 Evaluate side-chains 25 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.095 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: 0.0011 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 115 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 118 optimal weight: 0.0570 chunk 173 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 90 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 = 0.3613 r_free = 0.3613 target = 0.108594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093526 restraints weight = 20955.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097836 restraints weight = 9990.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100713 restraints weight = 5680.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102791 restraints weight = 3608.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104124 restraints weight = 2396.582| |-----------------------------------------------------------------------------| r_work (final): 0.3538 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.113907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099010 restraints weight = 11859.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.103210 restraints weight = 6294.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.106053 restraints weight = 3740.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.107849 restraints weight = 2396.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.109146 restraints weight = 1643.579| |-----------------------------------------------------------------------------| r_work (final): 0.3777 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.096355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.087922 restraints weight = 23540.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.090846 restraints weight = 12109.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.092663 restraints weight = 6873.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.093778 restraints weight = 4190.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.094602 restraints weight = 2763.279| |-----------------------------------------------------------------------------| r_work (final): 0.3804 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.084280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.083692 restraints weight = 358.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.084079 restraints weight = 80.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.084208 restraints weight = 25.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.084255 restraints weight = 8.952 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.084265 restraints weight = 3.840 | |-----------------------------------------------------------------------------| r_work (final): 0.3054 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.071609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.071568 restraints weight = 248.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.071600 restraints weight = 12.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.071599 restraints weight = 0.503 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.071599 restraints weight = 0.464 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.071599 restraints weight = 0.464 | |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 17997 Z= 0.212 Angle : 0.676 6.986 24459 Z= 0.367 Chirality : 0.042 0.163 2694 Planarity : 0.006 0.100 3132 Dihedral : 6.951 32.079 3075 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.16 % Allowed : 0.65 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.16), residues: 2172 helix: 0.11 (0.26), residues: 357 sheet: -1.80 (0.21), residues: 534 loop : -2.66 (0.15), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 576 TYR 0.022 0.002 TYR A 256 PHE 0.027 0.002 PHE D 570 TRP 0.009 0.001 TRP F 514 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (17943) covalent geometry : angle 0.66067 / 0.36 (24318) SS BOND : bond 0.02066 / 1.26 ( 21) SS BOND : angle 2.00353 / 1.27 ( 42) hydrogen bonds : bond 0.05007 / 3.38 ( 678) hydrogen bonds : angle 6.56055 / 4.62 ( 1962) link_BETA1-4 : bond 0.00368 / 0.20 ( 9) link_BETA1-4 : angle 1.42745 / 0.84 ( 27) link_NAG-ASN : bond 0.00777 / 0.48 ( 24) link_NAG-ASN : angle 2.20378 / 1.37 ( 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 59 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 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: C 70 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7670 (pt0) REVERT: C 83 ILE cc_start: 0.8692 (mt) cc_final: 0.8375 (mt) REVERT: C 98 HIS cc_start: 0.8431 (t70) cc_final: 0.7484 (t-90) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.0636 time to fit residues: 5.3230 Evaluate side-chains 45 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.138 Evaluate side-chains 40 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.073 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: B 589 ILE cc_start: 0.8202 (mt) cc_final: 0.7531 (tp) REVERT: B 590 ASP cc_start: 0.8585 (m-30) cc_final: 0.8276 (m-30) REVERT: B 620 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9057 (mm-30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0971 time to fit residues: 4.4249 Evaluate side-chains 34 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.069 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 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: H 17 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6344 (mm-30) REVERT: H 27 GLN cc_start: 0.7541 (mt0) cc_final: 0.7310 (mp10) REVERT: H 171 GLU cc_start: 0.5954 (pm20) cc_final: 0.4722 (pm20) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0817 time to fit residues: 2.6646 Evaluate side-chains 23 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.066 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 : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 1 optimal weight: 0.0010 chunk 170 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 20 optimal weight: 0.0060 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 90 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 = 0.3630 r_free = 0.3630 target = 0.109439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094441 restraints weight = 20444.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.098754 restraints weight = 9836.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.101609 restraints weight = 5620.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.103690 restraints weight = 3589.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.105064 restraints weight = 2391.626| |-----------------------------------------------------------------------------| r_work (final): 0.3555 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.115583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.101442 restraints weight = 11524.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105465 restraints weight = 6090.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.108104 restraints weight = 3594.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.109970 restraints weight = 2289.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.111113 restraints weight = 1549.636| |-----------------------------------------------------------------------------| r_work (final): 0.3799 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.096656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.088026 restraints weight = 20721.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.091131 restraints weight = 10389.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.093122 restraints weight = 5738.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.094251 restraints weight = 3356.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.095043 restraints weight = 2121.942| |-----------------------------------------------------------------------------| r_work (final): 0.3842 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.088283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087554 restraints weight = 371.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.087977 restraints weight = 87.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.088156 restraints weight = 29.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088235 restraints weight = 13.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088234 restraints weight = 5.435 | |-----------------------------------------------------------------------------| r_work (final): 0.3102 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.071350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.071316 restraints weight = 198.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.071343 restraints weight = 7.516 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.071339 restraints weight = 0.383 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 5)-----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.071339 restraints weight = 0.020 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.071312 restraints weight = 274.423| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17997 Z= 0.146 Angle : 0.664 6.600 24459 Z= 0.358 Chirality : 0.044 0.178 2694 Planarity : 0.008 0.179 3132 Dihedral : 6.703 30.379 3075 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.16 % Allowed : 0.65 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.16), residues: 2172 helix: 0.20 (0.26), residues: 357 sheet: -1.63 (0.21), residues: 534 loop : -2.63 (0.15), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 117 TYR 0.018 0.002 TYR E 256 PHE 0.018 0.002 PHE F 610 TRP 0.007 0.001 TRP C 64 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (17943) covalent geometry : angle 0.65164 / 0.36 (24318) SS BOND : bond 0.02011 / 1.22 ( 21) SS BOND : angle 1.68385 / 1.06 ( 42) hydrogen bonds : bond 0.05046 / 3.43 ( 678) hydrogen bonds : angle 6.52927 / 4.60 ( 1962) link_BETA1-4 : bond 0.00413 / 0.24 ( 9) link_BETA1-4 : angle 1.39990 / 0.82 ( 27) link_NAG-ASN : bond 0.00758 / 0.48 ( 24) link_NAG-ASN : angle 1.98217 / 1.22 ( 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 60 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.135 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: C 5 ASP cc_start: 0.7142 (t0) cc_final: 0.6628 (p0) REVERT: C 70 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7732 (pt0) REVERT: C 95 TYR cc_start: 0.7497 (t80) cc_final: 0.7265 (t80) REVERT: C 98 HIS cc_start: 0.8348 (t70) cc_final: 0.7838 (t70) REVERT: C 104 GLU cc_start: 0.8582 (mp0) cc_final: 0.7398 (mm-30) REVERT: C 199 ASN cc_start: 0.8785 (p0) cc_final: 0.8351 (p0) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.0615 time to fit residues: 5.2542 Evaluate side-chains 49 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.119 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 : 0.045 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: B 541 THR cc_start: 0.9122 (m) cc_final: 0.8849 (m) REVERT: B 589 ILE cc_start: 0.8133 (mt) cc_final: 0.7456 (tp) REVERT: B 619 TYR cc_start: 0.8038 (t80) cc_final: 0.7383 (t80) REVERT: B 620 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8955 (mm-30) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0692 time to fit residues: 3.3437 Evaluate side-chains 32 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.078 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 : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 17 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6282 (mm-30) REVERT: H 87 TYR cc_start: 0.4734 (m-80) cc_final: 0.4004 (m-80) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0832 time to fit residues: 2.9132 Evaluate side-chains 22 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 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: 0.0013 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 156 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 83 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.108702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.093943 restraints weight = 20658.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.098317 restraints weight = 10136.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101149 restraints weight = 5761.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.103170 restraints weight = 3645.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.104443 restraints weight = 2425.269| |-----------------------------------------------------------------------------| r_work (final): 0.3542 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.115095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.100883 restraints weight = 11804.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.104919 restraints weight = 6322.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.107508 restraints weight = 3745.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.109317 restraints weight = 2420.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.110519 restraints weight = 1662.581| |-----------------------------------------------------------------------------| r_work (final): 0.3771 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.097985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.090328 restraints weight = 23491.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.093139 restraints weight = 12293.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.094894 restraints weight = 6960.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.095972 restraints weight = 4140.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.096670 restraints weight = 2535.123| |-----------------------------------------------------------------------------| r_work (final): 0.3850 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.089008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.088424 restraints weight = 316.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.088778 restraints weight = 76.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.088931 restraints weight = 26.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.088974 restraints weight = 10.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.089007 restraints weight = 4.149 | |-----------------------------------------------------------------------------| r_work (final): 0.3108 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.072037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.072027 restraints weight = 216.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.072019 restraints weight = 10.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.072019 restraints weight = 1.017 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.072019 restraints weight = 1.012 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.072019 restraints weight = 1.012 | |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.6291 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= 0.141 Angle : 0.645 8.198 24459 Z= 0.347 Chirality : 0.043 0.171 2694 Planarity : 0.006 0.122 3132 Dihedral : 6.461 29.623 3075 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.16), residues: 2172 helix: 0.24 (0.25), residues: 360 sheet: -1.54 (0.21), residues: 534 loop : -2.56 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 576 TYR 0.020 0.002 TYR A 256 PHE 0.024 0.002 PHE B 570 TRP 0.015 0.001 TRP I 161 HIS 0.005 0.001 HIS I 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (17943) covalent geometry : angle 0.63294 / 0.34 (24318) SS BOND : bond 0.01998 / 1.21 ( 21) SS BOND : angle 1.59267 / 1.00 ( 42) hydrogen bonds : bond 0.04808 / 3.26 ( 678) hydrogen bonds : angle 6.29296 / 4.43 ( 1962) link_BETA1-4 : bond 0.00454 / 0.25 ( 9) link_BETA1-4 : angle 1.37157 / 0.78 ( 27) link_NAG-ASN : bond 0.00744 / 0.47 ( 24) link_NAG-ASN : angle 1.97090 / 1.21 ( 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 60 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 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: C 5 ASP cc_start: 0.7168 (t0) cc_final: 0.6631 (p0) REVERT: C 18 ASP cc_start: 0.7822 (m-30) cc_final: 0.7286 (t0) REVERT: C 70 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7431 (pt0) REVERT: C 95 TYR cc_start: 0.7779 (t80) cc_final: 0.7492 (t80) REVERT: C 98 HIS cc_start: 0.8691 (t70) cc_final: 0.8079 (t70) REVERT: C 107 GLU cc_start: 0.8692 (tt0) cc_final: 0.8410 (tt0) REVERT: C 199 ASN cc_start: 0.8757 (p0) cc_final: 0.8292 (p0) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.0624 time to fit residues: 5.3126 Evaluate side-chains 51 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.134 Evaluate side-chains 37 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.084 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: B 541 THR cc_start: 0.9153 (m) cc_final: 0.8869 (m) REVERT: B 589 ILE cc_start: 0.8263 (mt) cc_final: 0.7577 (tp) REVERT: B 590 ASP cc_start: 0.8688 (m-30) cc_final: 0.8350 (m-30) REVERT: B 620 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9013 (mm-30) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0684 time to fit residues: 3.0803 Evaluate side-chains 31 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.081 Evaluate side-chains 27 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.124 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: H 17 GLU cc_start: 0.6388 (mm-30) cc_final: 0.6126 (mm-30) REVERT: H 87 TYR cc_start: 0.4683 (m-80) cc_final: 0.3940 (m-80) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0810 time to fit residues: 2.7537 Evaluate side-chains 22 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 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: 0.0014 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 75 optimal weight: 0.0370 chunk 157 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 38 optimal weight: 0.0030 chunk 150 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.6070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.109248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095000 restraints weight = 21070.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.099212 restraints weight = 10550.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.102015 restraints weight = 6072.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.103862 restraints weight = 3821.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.105141 restraints weight = 2577.275| |-----------------------------------------------------------------------------| r_work (final): 0.3551 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.115790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.102040 restraints weight = 11733.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.106011 restraints weight = 6075.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.108539 restraints weight = 3569.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.110331 restraints weight = 2300.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.111439 restraints weight = 1567.349| |-----------------------------------------------------------------------------| r_work (final): 0.3798 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.100210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.093541 restraints weight = 25103.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.096047 restraints weight = 13046.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.097510 restraints weight = 7342.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.098434 restraints weight = 4366.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.099031 restraints weight = 2759.635| |-----------------------------------------------------------------------------| r_work (final): 0.3955 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.089233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.088510 restraints weight = 332.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.088899 restraints weight = 82.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.089021 restraints weight = 28.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.089083 restraints weight = 13.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.089085 restraints weight = 5.572 | |-----------------------------------------------------------------------------| r_work (final): 0.3106 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.063566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.063277 restraints weight = 266.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.063398 restraints weight = 51.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.063448 restraints weight = 11.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.063460 restraints weight = 2.766 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.063459 restraints weight = 0.697 | |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.6506 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= 0.127 Angle : 0.623 8.287 24459 Z= 0.333 Chirality : 0.043 0.173 2694 Planarity : 0.006 0.106 3132 Dihedral : 6.229 28.122 3075 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.16), residues: 2172 helix: 0.17 (0.25), residues: 360 sheet: -1.44 (0.21), residues: 555 loop : -2.49 (0.15), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 576 TYR 0.022 0.002 TYR E 256 PHE 0.029 0.002 PHE D 570 TRP 0.009 0.001 TRP A 127 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (17943) covalent geometry : angle 0.61264 / 0.33 (24318) SS BOND : bond 0.01991 / 1.21 ( 21) SS BOND : angle 1.46102 / 0.92 ( 42) hydrogen bonds : bond 0.04624 / 3.15 ( 678) hydrogen bonds : angle 6.16227 / 4.34 ( 1962) link_BETA1-4 : bond 0.00368 / 0.21 ( 9) link_BETA1-4 : angle 1.32300 / 0.76 ( 27) link_NAG-ASN : bond 0.00737 / 0.47 ( 24) link_NAG-ASN : angle 1.81586 / 1.11 ( 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 58 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 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: C 5 ASP cc_start: 0.7156 (t0) cc_final: 0.6624 (p0) REVERT: C 18 ASP cc_start: 0.7968 (m-30) cc_final: 0.7115 (t70) REVERT: C 70 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7452 (pt0) REVERT: C 95 TYR cc_start: 0.7820 (t80) cc_final: 0.7558 (t80) REVERT: C 98 HIS cc_start: 0.8484 (t70) cc_final: 0.7774 (t-170) REVERT: C 107 GLU cc_start: 0.8674 (tt0) cc_final: 0.8412 (tt0) REVERT: C 152 LEU cc_start: 0.8678 (mt) cc_final: 0.8164 (tp) REVERT: C 199 ASN cc_start: 0.8571 (p0) cc_final: 0.7997 (p0) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.0599 time to fit residues: 4.9524 Evaluate side-chains 54 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.144 Evaluate side-chains 36 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.070 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: B 541 THR cc_start: 0.9185 (m) cc_final: 0.8947 (p) REVERT: B 585 ASP cc_start: 0.8724 (m-30) cc_final: 0.8393 (m-30) REVERT: B 589 ILE cc_start: 0.8352 (mt) cc_final: 0.7618 (tp) REVERT: B 590 ASP cc_start: 0.8620 (m-30) cc_final: 0.8284 (m-30) REVERT: B 620 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8938 (mm-30) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0597 time to fit residues: 2.6815 Evaluate side-chains 31 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.074 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 : 0.095 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: I 87 TYR cc_start: 0.4512 (m-80) cc_final: 0.4214 (m-80) REVERT: I 131 GLU cc_start: 0.7590 (mp0) cc_final: 0.7152 (mp0) REVERT: I 138 GLN cc_start: 0.6397 (pm20) cc_final: 0.5977 (mp10) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0699 time to fit residues: 2.6533 Evaluate side-chains 25 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.091 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 184 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 160 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.109768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.095616 restraints weight = 19971.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099976 restraints weight = 9459.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.102812 restraints weight = 5252.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.104774 restraints weight = 3255.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106083 restraints weight = 2140.564| |-----------------------------------------------------------------------------| r_work (final): 0.3551 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.116220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.102346 restraints weight = 11553.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.106393 restraints weight = 5897.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.108949 restraints weight = 3424.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.110746 restraints weight = 2185.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.111893 restraints weight = 1478.394| |-----------------------------------------------------------------------------| r_work (final): 0.3816 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.097666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.090416 restraints weight = 23346.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.093152 restraints weight = 12128.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.094868 restraints weight = 6774.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.095864 restraints weight = 3962.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.096503 restraints weight = 2413.772| |-----------------------------------------------------------------------------| r_work (final): 0.3883 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.089967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.089281 restraints weight = 300.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.089590 restraints weight = 76.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.089845 restraints weight = 31.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.089931 restraints weight = 12.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.089943 restraints weight = 4.957 | |-----------------------------------------------------------------------------| r_work (final): 0.3119 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.063445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.062911 restraints weight = 345.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.063144 restraints weight = 95.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.063232 restraints weight = 29.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.063263 restraints weight = 10.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.063259 restraints weight = 4.051 | |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17997 Z= 0.127 Angle : 0.600 6.698 24459 Z= 0.321 Chirality : 0.042 0.168 2694 Planarity : 0.005 0.093 3132 Dihedral : 5.995 26.944 3075 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.17), residues: 2172 helix: 0.78 (0.26), residues: 342 sheet: -1.27 (0.22), residues: 522 loop : -2.42 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 576 TYR 0.019 0.001 TYR A 256 PHE 0.028 0.002 PHE F 570 TRP 0.016 0.001 TRP A 127 HIS 0.003 0.001 HIS B 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (17943) covalent geometry : angle 0.58864 / 0.32 (24318) SS BOND : bond 0.02004 / 1.23 ( 21) SS BOND : angle 1.53408 / 0.95 ( 42) hydrogen bonds : bond 0.04340 / 2.93 ( 678) hydrogen bonds : angle 5.99406 / 4.20 ( 1962) link_BETA1-4 : bond 0.00390 / 0.21 ( 9) link_BETA1-4 : angle 1.33566 / 0.78 ( 27) link_NAG-ASN : bond 0.00731 / 0.46 ( 24) link_NAG-ASN : angle 1.78711 / 1.09 ( 72) =============================================================================== Job complete usr+sys time: 2555.37 seconds wall clock time: 45 minutes 10.79 seconds (2710.79 seconds total)