Starting phenix.real_space_refine on Mon Sep 14 22:34:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5uk0_8562/09_2026/5uk0_8562_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5uk0_8562/09_2026/5uk0_8562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5uk0_8562/09_2026/5uk0_8562_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5uk0_8562/09_2026/5uk0_8562_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5uk0_8562/09_2026/5uk0_8562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5uk0_8562/09_2026/5uk0_8562.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.071 sd= 0.432 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 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33948 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "B" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "C" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "D" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "E" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "F" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "G" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "H" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "I" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.23, per 1000 atoms: 0.18 Number of scatterers: 33948 At special positions: 0 Unit cell: (141.04, 129.56, 182.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 3483 8.00 N 2985 7.00 C 11004 6.00 H 16401 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 637 " distance=2.19 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=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 648 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 637 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS D 644 " - pdb=" SG CYS D 648 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 637 " distance=1.84 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=2.03 Simple disulfide: pdb=" SG CYS F 644 " - pdb=" SG CYS F 648 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 406 " - " ASN A 129 " " NAG A 407 " - " ASN A 163 " " NAG A 408 " - " ASN A 15 " " NAG A 409 " - " ASN A 27 " " NAG A 410 " - " ASN A 290 " " NAG B 701 " - " ASN B 654 " " NAG C 406 " - " ASN C 129 " " NAG C 407 " - " ASN C 163 " " NAG C 408 " - " ASN C 15 " " NAG C 409 " - " ASN C 27 " " NAG C 410 " - " ASN C 290 " " NAG D 701 " - " ASN D 654 " " NAG E 406 " - " ASN E 129 " " NAG E 407 " - " ASN E 163 " " NAG E 408 " - " ASN E 15 " " NAG E 409 " - " ASN E 27 " " NAG E 410 " - " ASN E 290 " " NAG F 701 " - " ASN F 654 " " NAG J 1 " - " ASN A 91 " " NAG K 1 " - " ASN A 58 " " NAG L 1 " - " ASN C 91 " " NAG M 1 " - " ASN C 58 " " NAG N 1 " - " ASN E 91 " " NAG O 1 " - " ASN E 58 " Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 975.5 milliseconds 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 45 sheets defined 18.4% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 removed outlier: 3.941A 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: 4.367A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.967A 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: 3.790A pdb=" N GLN B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 626 " --> pdb=" O VAL B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 654 removed outlier: 3.556A pdb=" N ASN B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 670 Processing helix chain 'C' and resid 60 through 67 removed outlier: 3.941A 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: 4.366A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.966A 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: 3.790A pdb=" N GLN D 625 " --> pdb=" O LYS D 621 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 626 " --> pdb=" O VAL D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 654 removed outlier: 3.556A pdb=" N ASN D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'E' and resid 60 through 67 removed outlier: 3.941A 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: 4.367A pdb=" N TRP E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.966A 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: 3.789A pdb=" N GLN F 625 " --> pdb=" O LYS F 621 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 626 " --> pdb=" O VAL F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 654 removed outlier: 3.556A pdb=" N ASN F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 670 Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'H' and resid 80 through 84 Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'I' and resid 80 through 84 Processing helix chain 'I' and resid 211 through 215 Processing sheet with id=AA1, first strand: chain 'B' and resid 531 through 536 removed outlier: 3.989A 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: 4.258A pdb=" N ASP A 18 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR A 22 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 48 removed outlier: 5.828A pdb=" N LEU A 45 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 5.625A 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: 6.732A 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: 8.463A 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: 4.643A 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: 3.881A 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: 3.989A 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: 4.258A pdb=" N ASP C 18 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR C 22 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 48 removed outlier: 5.828A pdb=" N LEU C 45 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 5.624A 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: 6.733A 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: 8.463A 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: 4.643A 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: 3.881A 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: 3.989A 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: 4.257A pdb=" N ASP E 18 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR E 22 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 48 removed outlier: 5.827A pdb=" N LEU E 45 " --> pdb=" O ASP E 276 " (cutoff:3.500A) removed outlier: 5.624A 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: 6.733A 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: 8.464A 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: 4.642A 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: 3.882A pdb=" N CYS E 282 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.192A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'G' and resid 129 through 132 Processing sheet with id=AD8, first strand: chain 'G' and resid 136 through 137 removed outlier: 5.033A pdb=" N ASP G 158 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET G 159 " --> pdb=" O GLY G 175 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY G 175 " --> pdb=" O MET G 159 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TRP G 161 " --> pdb=" O VAL G 173 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 173 " --> pdb=" O TRP G 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.192A pdb=" N GLN H 38 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU H 47 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE3, first strand: chain 'H' and resid 129 through 132 Processing sheet with id=AE4, first strand: chain 'H' and resid 136 through 137 removed outlier: 5.034A pdb=" N ASP H 158 " --> pdb=" O GLY H 223 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET H 159 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY H 175 " --> pdb=" O MET H 159 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TRP H 161 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 173 " --> pdb=" O TRP H 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.192A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AE8, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AE9, first strand: chain 'I' and resid 136 through 137 removed outlier: 5.034A pdb=" N ASP I 158 " --> pdb=" O GLY I 223 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET I 159 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY I 175 " --> pdb=" O MET I 159 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TRP I 161 " --> pdb=" O VAL I 173 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL I 173 " --> pdb=" O TRP I 161 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 1926 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: 8.46 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 16395 1.02 - 1.22: 9 1.22 - 1.42: 7681 1.42 - 1.62: 10157 1.62 - 1.82: 102 Bond restraints: 34344 Sorted by residual: bond pdb=" CA GLN I 90 " pdb=" CB GLN I 90 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.50e-02 4.44e+03 1.36e+01 bond pdb=" CA GLN G 90 " pdb=" CB GLN G 90 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.50e-02 4.44e+03 1.32e+01 bond pdb=" CA GLN H 90 " pdb=" CB GLN H 90 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.50e-02 4.44e+03 1.31e+01 bond pdb=" CB TYR G 32 " pdb=" HB2 TYR G 32 " ideal model delta sigma weight residual 0.970 0.918 0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" CA TRP I 36 " pdb=" CB TRP I 36 " ideal model delta sigma weight residual 1.532 1.486 0.045 1.82e-02 3.02e+03 6.23e+00 ... (remaining 34339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 57104 2.28 - 4.56: 3939 4.56 - 6.83: 458 6.83 - 9.11: 51 9.11 - 11.39: 5 Bond angle restraints: 61557 Sorted by residual: angle pdb=" N GLY H 31 " pdb=" CA GLY H 31 " pdb=" C GLY H 31 " ideal model delta sigma weight residual 115.30 126.69 -11.39 1.44e+00 4.82e-01 6.26e+01 angle pdb=" N GLY G 31 " pdb=" CA GLY G 31 " pdb=" C GLY G 31 " ideal model delta sigma weight residual 115.30 126.68 -11.38 1.44e+00 4.82e-01 6.25e+01 angle pdb=" N GLY I 31 " pdb=" CA GLY I 31 " pdb=" C GLY I 31 " ideal model delta sigma weight residual 115.30 126.63 -11.33 1.44e+00 4.82e-01 6.19e+01 angle pdb=" C GLU I 1 " pdb=" N ILE I 2 " pdb=" CA ILE I 2 " ideal model delta sigma weight residual 120.35 129.48 -9.13 1.39e+00 5.18e-01 4.32e+01 angle pdb=" C GLU H 1 " pdb=" N ILE H 2 " pdb=" CA ILE H 2 " ideal model delta sigma weight residual 120.35 129.48 -9.13 1.39e+00 5.18e-01 4.31e+01 ... (remaining 61552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.13: 15466 19.13 - 38.25: 984 38.25 - 57.38: 280 57.38 - 76.51: 55 76.51 - 95.64: 21 Dihedral angle restraints: 16806 sinusoidal: 9345 harmonic: 7461 Sorted by residual: dihedral pdb=" CA SER G 53 " pdb=" C SER G 53 " pdb=" N SER G 54 " pdb=" CA SER G 54 " ideal model delta harmonic sigma weight residual 180.00 -146.83 -33.17 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA SER I 53 " pdb=" C SER I 53 " pdb=" N SER I 54 " pdb=" CA SER I 54 " ideal model delta harmonic sigma weight residual -180.00 -146.85 -33.15 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA SER H 53 " pdb=" C SER H 53 " pdb=" N SER H 54 " pdb=" CA SER H 54 " ideal model delta harmonic sigma weight residual -180.00 -146.85 -33.15 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 16803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2240 0.084 - 0.167: 411 0.167 - 0.251: 28 0.251 - 0.335: 12 0.335 - 0.418: 3 Chirality restraints: 2694 Sorted by residual: 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 6.94e+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 -2.24 -0.16 2.00e-02 2.50e+03 6.47e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.36e+01 ... (remaining 2691 not shown) Planarity restraints: 5244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 42 " 0.150 2.00e-02 2.50e+03 1.61e-01 3.89e+02 pdb=" CG ASN A 42 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 42 " -0.133 2.00e-02 2.50e+03 pdb=" ND2 ASN A 42 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 42 " -0.235 2.00e-02 2.50e+03 pdb="HD22 ASN A 42 " 0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 42 " -0.149 2.00e-02 2.50e+03 1.61e-01 3.87e+02 pdb=" CG ASN C 42 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 42 " 0.133 2.00e-02 2.50e+03 pdb=" ND2 ASN C 42 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN C 42 " 0.234 2.00e-02 2.50e+03 pdb="HD22 ASN C 42 " -0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 42 " 0.149 2.00e-02 2.50e+03 1.60e-01 3.84e+02 pdb=" CG ASN E 42 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN E 42 " -0.132 2.00e-02 2.50e+03 pdb=" ND2 ASN E 42 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN E 42 " -0.233 2.00e-02 2.50e+03 pdb="HD22 ASN E 42 " 0.243 2.00e-02 2.50e+03 ... (remaining 5241 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 7678 2.31 - 2.88: 76842 2.88 - 3.46: 85102 3.46 - 4.03: 117934 4.03 - 4.60: 177128 Nonbonded interactions: 464684 Sorted by model distance: nonbonded pdb=" HE ARG D 576 " pdb=" OE2 GLU E 104 " model vdw 1.738 2.450 nonbonded pdb=" HE2 HIS C 130 " pdb=" O PRO C 162 " model vdw 1.743 2.450 nonbonded pdb=" HE2 HIS A 130 " pdb=" O PRO A 162 " model vdw 1.743 2.450 nonbonded pdb=" HE2 HIS E 130 " pdb=" O PRO E 162 " model vdw 1.743 2.450 nonbonded pdb=" O LEU G 176 " pdb="HH22 ARG G 196 " model vdw 1.754 2.450 ... (remaining 464679 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.610 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.196 17997 Z= 0.452 Angle : 1.284 11.390 24459 Z= 0.741 Chirality : 0.064 0.418 2694 Planarity : 0.009 0.082 3132 Dihedral : 12.083 95.637 7023 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.29 % Favored : 91.57 % 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 : 0.72 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.15), residues: 2172 helix: -0.82 (0.24), residues: 327 sheet: -2.81 (0.18), residues: 528 loop : -2.70 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG I 222 TYR 0.028 0.004 TYR E 161 PHE 0.038 0.004 PHE F 509 TRP 0.021 0.005 TRP C 153 HIS 0.023 0.004 HIS F 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00979 / 0.44 (17943) covalent geometry : angle 1.26415 / 0.74 (24318) SS BOND : bond 0.05490 / 3.63 ( 21) SS BOND : angle 2.16022 / 1.28 ( 42) hydrogen bonds : bond 0.09708 / 6.41 ( 672) hydrogen bonds : angle 10.70184 / 7.39 ( 1926) link_BETA1-4 : bond 0.01216 / 0.63 ( 9) link_BETA1-4 : angle 3.79759 / 2.32 ( 27) link_NAG-ASN : bond 0.01096 / 0.68 ( 24) link_NAG-ASN : angle 3.54096 / 2.27 ( 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 91 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8694 (p0) cc_final: 0.8433 (p0) REVERT: A 116 GLU cc_start: 0.9055 (pt0) cc_final: 0.8824 (pt0) REVERT: A 119 GLU cc_start: 0.8490 (tt0) cc_final: 0.8052 (pm20) REVERT: A 151 LEU cc_start: 0.8487 (mt) cc_final: 0.8184 (mt) REVERT: A 171 ASN cc_start: 0.8488 (p0) cc_final: 0.8205 (t0) REVERT: A 199 ASN cc_start: 0.9283 (m-40) cc_final: 0.8905 (t0) outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.1320 time to fit residues: 14.2719 Evaluate side-chains 58 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.135 Evaluate side-chains 69 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 548 ILE cc_start: 0.8946 (mm) cc_final: 0.8729 (tt) REVERT: B 561 THR cc_start: 0.8029 (p) cc_final: 0.7719 (t) REVERT: B 589 ILE cc_start: 0.9031 (mt) cc_final: 0.8721 (tp) REVERT: B 606 ARG cc_start: 0.8385 (mmm160) cc_final: 0.7856 (mmt-90) REVERT: B 608 LEU cc_start: 0.9418 (mt) cc_final: 0.9151 (tp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1163 time to fit residues: 8.8844 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 : 0.082 Evaluate side-chains 48 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2320 time to fit residues: 12.0352 Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.094 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=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.0060 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.110531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094351 restraints weight = 22252.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.099210 restraints weight = 10155.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.102401 restraints weight = 5579.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.104568 restraints weight = 3420.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106072 restraints weight = 2241.867| |-----------------------------------------------------------------------------| r_work (final): 0.3681 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.104732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.092044 restraints weight = 11804.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.095434 restraints weight = 6374.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.097769 restraints weight = 3709.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.099037 restraints weight = 2303.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.100111 restraints weight = 1612.971| |-----------------------------------------------------------------------------| r_work (final): 0.3784 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.082997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.073022 restraints weight = 20912.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.076317 restraints weight = 10372.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.078563 restraints weight = 5738.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.080025 restraints weight = 3349.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.081016 restraints weight = 2043.914| |-----------------------------------------------------------------------------| r_work (final): 0.3757 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.076499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.074993 restraints weight = 437.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.075534 restraints weight = 152.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.075897 restraints weight = 83.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.076037 restraints weight = 51.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.076162 restraints weight = 35.059| |-----------------------------------------------------------------------------| r_work (final): 0.2959 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.083792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.077165 restraints weight = 232.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.077722 restraints weight = 125.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.078062 restraints weight = 70.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.078216 restraints weight = 39.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.078260 restraints weight = 24.583| |-----------------------------------------------------------------------------| r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 17997 Z= 0.214 Angle : 0.837 8.863 24459 Z= 0.456 Chirality : 0.047 0.276 2694 Planarity : 0.008 0.098 3132 Dihedral : 10.281 58.052 3075 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.32 % Allowed : 2.10 % Favored : 97.57 % 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: -3.28 (0.15), residues: 2172 helix: -0.05 (0.27), residues: 339 sheet: -2.54 (0.18), residues: 546 loop : -2.70 (0.14), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 220 TYR 0.028 0.002 TYR G 33 PHE 0.018 0.002 PHE B 509 TRP 0.011 0.002 TRP F 592 HIS 0.008 0.001 HIS I 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (17943) covalent geometry : angle 0.82102 / 0.45 (24318) SS BOND : bond 0.05369 / 3.52 ( 21) SS BOND : angle 2.03880 / 1.29 ( 42) hydrogen bonds : bond 0.05397 / 3.50 ( 672) hydrogen bonds : angle 8.17577 / 5.68 ( 1926) link_BETA1-4 : bond 0.00539 / 0.31 ( 9) link_BETA1-4 : angle 1.98066 / 1.14 ( 27) link_NAG-ASN : bond 0.00333 / 0.21 ( 24) link_NAG-ASN : angle 2.54543 / 1.66 ( 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 83 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 GLU cc_start: 0.8772 (tt0) cc_final: 0.8421 (tm-30) REVERT: E 39 ASP cc_start: 0.8771 (p0) cc_final: 0.8561 (p0) REVERT: E 116 GLU cc_start: 0.9220 (pt0) cc_final: 0.8858 (pp20) REVERT: E 119 GLU cc_start: 0.9099 (tt0) cc_final: 0.8861 (tp30) REVERT: E 152 LEU cc_start: 0.8876 (mt) cc_final: 0.8500 (mp) REVERT: E 171 ASN cc_start: 0.9036 (p0) cc_final: 0.8773 (t0) REVERT: E 199 ASN cc_start: 0.9558 (m-40) cc_final: 0.8874 (t0) REVERT: E 255 ARG cc_start: 0.7209 (ttt180) cc_final: 0.6909 (ttp-170) outliers start: 2 outliers final: 1 residues processed: 82 average time/residue: 0.1169 time to fit residues: 11.5737 Evaluate side-chains 66 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.104 Evaluate side-chains 59 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 511 GLU cc_start: 0.8156 (pm20) cc_final: 0.7596 (tp30) REVERT: F 552 VAL cc_start: 0.9111 (t) cc_final: 0.8861 (m) REVERT: F 556 ILE cc_start: 0.8764 (pt) cc_final: 0.8036 (pt) REVERT: F 557 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8600 (mp0) REVERT: F 561 THR cc_start: 0.8060 (p) cc_final: 0.7766 (t) REVERT: F 594 TYR cc_start: 0.8806 (t80) cc_final: 0.8195 (m-80) REVERT: F 598 LEU cc_start: 0.9401 (mt) cc_final: 0.8928 (mt) REVERT: F 620 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8796 (tp30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1003 time to fit residues: 6.6668 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 : 0.070 Evaluate side-chains 37 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 195 SER cc_start: 0.8439 (t) cc_final: 0.8191 (p) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1541 time to fit residues: 6.4242 Evaluate side-chains 29 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.060 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0008 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 150 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 33 optimal weight: 0.0270 chunk 143 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 158 ASN F 526 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.112823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098994 restraints weight = 19070.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.103297 restraints weight = 8992.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.106127 restraints weight = 4968.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.108032 restraints weight = 3040.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.109214 restraints weight = 1963.521| |-----------------------------------------------------------------------------| r_work (final): 0.3716 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.113344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.100321 restraints weight = 13397.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.104529 restraints weight = 6766.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.107135 restraints weight = 3710.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.108861 restraints weight = 2205.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.110036 restraints weight = 1381.423| |-----------------------------------------------------------------------------| r_work (final): 0.3872 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.081575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.071662 restraints weight = 21775.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.074896 restraints weight = 10563.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.076927 restraints weight = 5772.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.078353 restraints weight = 3491.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.079228 restraints weight = 2190.762| |-----------------------------------------------------------------------------| r_work (final): 0.3718 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.077788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.077181 restraints weight = 445.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.077530 restraints weight = 101.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.077667 restraints weight = 34.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.077751 restraints weight = 15.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.077768 restraints weight = 5.605 | |-----------------------------------------------------------------------------| r_work (final): 0.2961 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.085202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.078707 restraints weight = 216.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.078304 restraints weight = 235.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.077915 restraints weight = 255.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.077554 restraints weight = 275.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 9)-----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.077197 restraints weight = 293.921| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 17997 Z= 0.218 Angle : 0.783 6.953 24459 Z= 0.426 Chirality : 0.045 0.266 2694 Planarity : 0.008 0.142 3132 Dihedral : 8.944 38.772 3075 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.49 % Allowed : 1.46 % Favored : 98.06 % 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: -3.29 (0.16), residues: 2172 helix: -0.37 (0.26), residues: 345 sheet: -2.44 (0.20), residues: 504 loop : -2.70 (0.14), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 606 TYR 0.035 0.002 TYR G 33 PHE 0.017 0.002 PHE F 503 TRP 0.012 0.002 TRP B 592 HIS 0.021 0.002 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (17943) covalent geometry : angle 0.76089 / 0.42 (24318) SS BOND : bond 0.05196 / 3.24 ( 21) SS BOND : angle 2.87701 / 1.75 ( 42) hydrogen bonds : bond 0.05282 / 3.45 ( 672) hydrogen bonds : angle 7.60300 / 5.27 ( 1926) link_BETA1-4 : bond 0.00665 / 0.37 ( 9) link_BETA1-4 : angle 2.06498 / 1.17 ( 27) link_NAG-ASN : bond 0.00546 / 0.34 ( 24) link_NAG-ASN : angle 2.49171 / 1.61 ( 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 75 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.9103 (t0) cc_final: 0.8755 (t0) REVERT: A 103 GLU cc_start: 0.8375 (pt0) cc_final: 0.7922 (tt0) REVERT: A 151 LEU cc_start: 0.8953 (mt) cc_final: 0.8654 (mt) REVERT: A 171 ASN cc_start: 0.8394 (p0) cc_final: 0.8187 (t0) REVERT: A 199 ASN cc_start: 0.9067 (m-40) cc_final: 0.8843 (t0) REVERT: A 208 HIS cc_start: 0.8804 (m90) cc_final: 0.8412 (m-70) outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 0.1188 time to fit residues: 10.8300 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 : 0.098 Evaluate side-chains 56 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 572 LYS cc_start: 0.7979 (pttm) cc_final: 0.6910 (tptt) REVERT: D 583 LYS cc_start: 0.7073 (tttt) cc_final: 0.6497 (ttmt) REVERT: D 598 LEU cc_start: 0.9473 (mt) cc_final: 0.9265 (tt) REVERT: D 611 HIS cc_start: 0.8004 (m170) cc_final: 0.7178 (m170) REVERT: D 637 CYS cc_start: 0.8968 (m) cc_final: 0.8406 (t) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.1017 time to fit residues: 6.4641 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 : 0.075 Evaluate side-chains 32 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.095 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 195 SER cc_start: 0.8782 (t) cc_final: 0.8510 (p) REVERT: I 235 PHE cc_start: 0.8440 (p90) cc_final: 0.8032 (p90) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1487 time to fit residues: 5.4082 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 : 0.076 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: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 142 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 125 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 136 optimal weight: 0.0000 chunk 150 optimal weight: 0.0170 chunk 176 optimal weight: 0.9980 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.113514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.099509 restraints weight = 19383.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.103944 restraints weight = 9063.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.106874 restraints weight = 4998.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108796 restraints weight = 3029.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.110098 restraints weight = 1962.703| |-----------------------------------------------------------------------------| r_work (final): 0.3723 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.132872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.115232 restraints weight = 12202.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.120073 restraints weight = 5896.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.123360 restraints weight = 3382.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.125626 restraints weight = 2118.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.127204 restraints weight = 1420.191| |-----------------------------------------------------------------------------| r_work (final): 0.3841 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.080688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.070596 restraints weight = 23829.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073937 restraints weight = 10834.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.076066 restraints weight = 5706.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.077453 restraints weight = 3314.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.078227 restraints weight = 2034.509| |-----------------------------------------------------------------------------| r_work (final): 0.3730 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.085279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.083600 restraints weight = 344.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.084489 restraints weight = 178.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.084927 restraints weight = 81.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.085116 restraints weight = 37.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.085192 restraints weight = 16.169| |-----------------------------------------------------------------------------| r_work (final): 0.3207 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.054789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.054502 restraints weight = 252.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.054682 restraints weight = 54.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.054736 restraints weight = 13.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.054754 restraints weight = 5.861 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.054756 restraints weight = 2.270 | |-----------------------------------------------------------------------------| r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17997 Z= 0.142 Angle : 0.698 9.098 24459 Z= 0.379 Chirality : 0.044 0.201 2694 Planarity : 0.006 0.047 3132 Dihedral : 7.784 33.164 3075 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % 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 : 0.00 % 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: -2.96 (0.16), residues: 2172 helix: 0.38 (0.27), residues: 342 sheet: -2.23 (0.21), residues: 507 loop : -2.62 (0.14), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 77 TYR 0.029 0.002 TYR I 33 PHE 0.015 0.002 PHE D 610 TRP 0.010 0.001 TRP G 36 HIS 0.013 0.002 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (17943) covalent geometry : angle 0.68073 / 0.37 (24318) SS BOND : bond 0.00715 / 0.44 ( 21) SS BOND : angle 2.60886 / 1.55 ( 42) hydrogen bonds : bond 0.04754 / 3.09 ( 672) hydrogen bonds : angle 7.06451 / 4.92 ( 1926) link_BETA1-4 : bond 0.00310 / 0.18 ( 9) link_BETA1-4 : angle 1.53855 / 0.88 ( 27) link_NAG-ASN : bond 0.00320 / 0.21 ( 24) link_NAG-ASN : angle 2.05193 / 1.33 ( 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 70 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8998 (t0) cc_final: 0.8555 (t0) REVERT: A 103 GLU cc_start: 0.8465 (pt0) cc_final: 0.7940 (tt0) REVERT: A 151 LEU cc_start: 0.8931 (mt) cc_final: 0.8714 (mt) REVERT: A 171 ASN cc_start: 0.8581 (p0) cc_final: 0.8207 (t0) REVERT: A 208 HIS cc_start: 0.8771 (m90) cc_final: 0.8408 (m-70) outliers start: 3 outliers final: 1 residues processed: 70 average time/residue: 0.0900 time to fit residues: 8.1617 Evaluate side-chains 55 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.138 Evaluate side-chains 49 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 556 ILE cc_start: 0.8961 (pt) cc_final: 0.8467 (pt) REVERT: D 557 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8136 (mp0) REVERT: D 572 LYS cc_start: 0.8124 (pttm) cc_final: 0.7060 (tptt) REVERT: D 583 LYS cc_start: 0.7159 (tttt) cc_final: 0.6823 (ttmt) REVERT: D 611 HIS cc_start: 0.7722 (m170) cc_final: 0.7466 (m170) REVERT: D 637 CYS cc_start: 0.8043 (m) cc_final: 0.7189 (t) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1171 time to fit residues: 6.4286 Evaluate side-chains 39 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.078 Evaluate side-chains 32 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 155 ASN cc_start: 0.9179 (m-40) cc_final: 0.8953 (m110) REVERT: H 195 SER cc_start: 0.9236 (t) cc_final: 0.8701 (m) REVERT: H 205 LEU cc_start: 0.8616 (tp) cc_final: 0.8366 (tp) REVERT: H 235 PHE cc_start: 0.8784 (p90) cc_final: 0.8140 (p90) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1342 time to fit residues: 4.9545 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 : 0.105 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 156 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 193 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 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 = 0.3727 r_free = 0.3727 target = 0.110745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.097351 restraints weight = 19784.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.101630 restraints weight = 9582.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104412 restraints weight = 5378.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106265 restraints weight = 3280.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.107476 restraints weight = 2123.842| |-----------------------------------------------------------------------------| r_work (final): 0.3678 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.110898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.096463 restraints weight = 12949.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.100808 restraints weight = 6237.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.103605 restraints weight = 3469.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.105396 restraints weight = 2093.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.106632 restraints weight = 1361.630| |-----------------------------------------------------------------------------| r_work (final): 0.3803 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.079635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.069266 restraints weight = 28342.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.072713 restraints weight = 13999.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.074935 restraints weight = 7728.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.076328 restraints weight = 4613.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.077189 restraints weight = 2917.352| |-----------------------------------------------------------------------------| r_work (final): 0.3684 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080760 restraints weight = 419.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081687 restraints weight = 256.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.082534 restraints weight = 183.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.083089 restraints weight = 118.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.083451 restraints weight = 75.898| |-----------------------------------------------------------------------------| r_work (final): 0.3163 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.085526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.079788 restraints weight = 196.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.080435 restraints weight = 95.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.080707 restraints weight = 50.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.080885 restraints weight = 28.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.081005 restraints weight = 16.234| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 17997 Z= 0.208 Angle : 0.708 12.104 24459 Z= 0.383 Chirality : 0.043 0.195 2694 Planarity : 0.005 0.042 3132 Dihedral : 7.302 32.588 3075 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.32 % Allowed : 1.94 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.16), residues: 2172 helix: 0.76 (0.28), residues: 345 sheet: -2.21 (0.21), residues: 519 loop : -2.67 (0.14), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 606 TYR 0.030 0.002 TYR G 33 PHE 0.023 0.002 PHE D 570 TRP 0.009 0.001 TRP G 36 HIS 0.006 0.002 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (17943) covalent geometry : angle 0.68581 / 0.38 (24318) SS BOND : bond 0.04339 / 2.59 ( 21) SS BOND : angle 3.33329 / 2.03 ( 42) hydrogen bonds : bond 0.04760 / 3.05 ( 672) hydrogen bonds : angle 6.75183 / 4.69 ( 1926) link_BETA1-4 : bond 0.00270 / 0.15 ( 9) link_BETA1-4 : angle 1.51633 / 0.86 ( 27) link_NAG-ASN : bond 0.00403 / 0.26 ( 24) link_NAG-ASN : angle 2.04545 / 1.32 ( 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 67 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8999 (t0) cc_final: 0.8496 (t0) REVERT: A 103 GLU cc_start: 0.8369 (pt0) cc_final: 0.7896 (tt0) REVERT: A 151 LEU cc_start: 0.9017 (mt) cc_final: 0.8768 (mt) REVERT: A 171 ASN cc_start: 0.8416 (p0) cc_final: 0.8081 (t0) REVERT: A 208 HIS cc_start: 0.8840 (m90) cc_final: 0.8510 (m-70) REVERT: A 237 LEU cc_start: 0.9323 (tp) cc_final: 0.8902 (tp) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 0.0908 time to fit residues: 7.8159 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 : 0.141 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 : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 568 LYS cc_start: 0.8101 (tptp) cc_final: 0.7368 (mmtm) REVERT: D 570 PHE cc_start: 0.7798 (m-10) cc_final: 0.6447 (m-10) REVERT: D 572 LYS cc_start: 0.8202 (pttm) cc_final: 0.7058 (tptt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0834 time to fit residues: 4.2291 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 : 0.074 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 : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1410 time to fit residues: 4.4945 Evaluate side-chains 21 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.056 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: 0.0009 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 40 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 34 optimal weight: 0.0870 chunk 49 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.111656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098297 restraints weight = 19724.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102534 restraints weight = 9476.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105290 restraints weight = 5284.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.107096 restraints weight = 3230.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108258 restraints weight = 2108.082| |-----------------------------------------------------------------------------| r_work (final): 0.3694 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.109391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.096611 restraints weight = 12101.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.100708 restraints weight = 6049.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.103224 restraints weight = 3338.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.104899 restraints weight = 2008.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.105907 restraints weight = 1275.898| |-----------------------------------------------------------------------------| r_work (final): 0.3810 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.077420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.067384 restraints weight = 28360.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.070695 restraints weight = 13957.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.072899 restraints weight = 7660.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.074173 restraints weight = 4518.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.075108 restraints weight = 2908.904| |-----------------------------------------------------------------------------| r_work (final): 0.3700 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.071189 restraints weight = 313.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.072024 restraints weight = 212.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.072578 restraints weight = 165.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.072578 restraints weight = 138.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.072578 restraints weight = 138.636| |-----------------------------------------------------------------------------| r_work (final): 0.2955 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.086389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.080188 restraints weight = 157.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.080735 restraints weight = 76.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.080961 restraints weight = 42.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.081143 restraints weight = 24.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.081227 restraints weight = 14.455| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17997 Z= 0.153 Angle : 0.665 11.112 24459 Z= 0.361 Chirality : 0.042 0.185 2694 Planarity : 0.005 0.039 3132 Dihedral : 6.961 32.395 3075 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.32 % Allowed : 0.97 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.16), residues: 2172 helix: 0.97 (0.28), residues: 342 sheet: -1.97 (0.20), residues: 537 loop : -2.60 (0.15), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.027 0.002 TYR G 33 PHE 0.014 0.001 PHE D 570 TRP 0.009 0.001 TRP H 36 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (17943) covalent geometry : angle 0.64327 / 0.35 (24318) SS BOND : bond 0.01476 / 0.75 ( 21) SS BOND : angle 3.19883 / 1.85 ( 42) hydrogen bonds : bond 0.04638 / 2.99 ( 672) hydrogen bonds : angle 6.61545 / 4.62 ( 1926) link_BETA1-4 : bond 0.00371 / 0.21 ( 9) link_BETA1-4 : angle 1.41486 / 0.82 ( 27) link_NAG-ASN : bond 0.00326 / 0.22 ( 24) link_NAG-ASN : angle 1.88742 / 1.22 ( 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 66 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.165 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: A 35 ASN cc_start: 0.8988 (t0) cc_final: 0.8620 (t0) REVERT: A 103 GLU cc_start: 0.8141 (pt0) cc_final: 0.7754 (tt0) REVERT: A 151 LEU cc_start: 0.9009 (mt) cc_final: 0.8741 (mt) REVERT: A 171 ASN cc_start: 0.8449 (p0) cc_final: 0.8012 (t0) REVERT: A 208 HIS cc_start: 0.8833 (m90) cc_final: 0.8519 (m-70) REVERT: A 237 LEU cc_start: 0.9301 (tp) cc_final: 0.8951 (tp) outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 0.0722 time to fit residues: 6.3544 Evaluate side-chains 52 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.142 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 : 0.049 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: D 524 TYR cc_start: 0.7430 (m-80) cc_final: 0.6567 (t80) REVERT: D 568 LYS cc_start: 0.8054 (tptp) cc_final: 0.7101 (mmtm) REVERT: D 570 PHE cc_start: 0.7647 (m-10) cc_final: 0.6455 (m-10) REVERT: D 572 LYS cc_start: 0.8344 (pttm) cc_final: 0.7181 (tptt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0807 time to fit residues: 4.0690 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 : 0.070 Evaluate side-chains 28 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 155 ASN cc_start: 0.9274 (p0) cc_final: 0.9007 (p0) REVERT: I 160 HIS cc_start: 0.8283 (m-70) cc_final: 0.7766 (m-70) REVERT: I 207 MET cc_start: 0.8216 (mpp) cc_final: 0.7476 (mpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1361 time to fit residues: 4.3596 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 : 0.074 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 46 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 113 optimal weight: 0.0770 chunk 56 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 38 optimal weight: 0.0010 chunk 153 optimal weight: 0.6980 overall best weight: 1.2746 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.112036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095884 restraints weight = 22273.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100666 restraints weight = 10875.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.104011 restraints weight = 6245.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.106221 restraints weight = 3906.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107698 restraints weight = 2602.253| |-----------------------------------------------------------------------------| r_work (final): 0.3633 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.153047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.144951 restraints weight = 19950.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.146696 restraints weight = 9572.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.147698 restraints weight = 5048.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.148326 restraints weight = 3014.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.148704 restraints weight = 2034.956| |-----------------------------------------------------------------------------| r_work (final): 0.4122 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.079868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.070337 restraints weight = 21996.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.073376 restraints weight = 10539.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.075393 restraints weight = 5819.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.076618 restraints weight = 3463.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.077186 restraints weight = 2259.258| |-----------------------------------------------------------------------------| r_work (final): 0.3714 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.075593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.070099 restraints weight = 270.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.070934 restraints weight = 188.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.071553 restraints weight = 149.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.072102 restraints weight = 123.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.072433 restraints weight = 104.234| |-----------------------------------------------------------------------------| r_work (final): 0.3010 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2344 r_free = 0.2344 target = 0.050535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.050096 restraints weight = 276.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.050263 restraints weight = 50.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.050288 restraints weight = 15.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.050326 restraints weight = 12.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.050325 restraints weight = 10.029| |-----------------------------------------------------------------------------| r_work (final): 0.2341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 17997 Z= 0.160 Angle : 0.653 16.505 24459 Z= 0.353 Chirality : 0.042 0.207 2694 Planarity : 0.005 0.038 3132 Dihedral : 6.671 31.368 3075 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.29 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 : 0.00 % 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: -2.61 (0.16), residues: 2172 helix: 1.12 (0.29), residues: 342 sheet: -1.86 (0.21), residues: 537 loop : -2.60 (0.15), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 77 TYR 0.028 0.002 TYR H 33 PHE 0.014 0.001 PHE F 638 TRP 0.011 0.001 TRP I 36 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (17943) covalent geometry : angle 0.62059 / 0.34 (24318) SS BOND : bond 0.03779 / 2.23 ( 21) SS BOND : angle 4.37167 / 2.67 ( 42) hydrogen bonds : bond 0.04566 / 2.95 ( 672) hydrogen bonds : angle 6.36182 / 4.41 ( 1926) link_BETA1-4 : bond 0.00323 / 0.17 ( 9) link_BETA1-4 : angle 1.30076 / 0.75 ( 27) link_NAG-ASN : bond 0.00292 / 0.19 ( 24) link_NAG-ASN : angle 1.77038 / 1.14 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.158 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: A 59 CYS cc_start: 0.7988 (m) cc_final: 0.7755 (m) REVERT: A 103 GLU cc_start: 0.8332 (pt0) cc_final: 0.7806 (tt0) REVERT: A 171 ASN cc_start: 0.8769 (p0) cc_final: 0.8490 (t0) REVERT: A 208 HIS cc_start: 0.9196 (m90) cc_final: 0.8927 (m-70) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.0727 time to fit residues: 6.3532 Evaluate side-chains 53 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.095 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 : 0.062 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: D 524 TYR cc_start: 0.7220 (m-80) cc_final: 0.6409 (t80) REVERT: D 568 LYS cc_start: 0.7838 (tptp) cc_final: 0.6766 (mmtm) REVERT: D 570 PHE cc_start: 0.7624 (m-10) cc_final: 0.6598 (m-10) REVERT: D 583 LYS cc_start: 0.6951 (tttt) cc_final: 0.6138 (ttmt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0780 time to fit residues: 3.9284 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 : 0.074 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 : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 155 ASN cc_start: 0.9214 (p0) cc_final: 0.8923 (p0) REVERT: I 160 HIS cc_start: 0.8354 (m-70) cc_final: 0.7778 (m-70) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1302 time to fit residues: 4.0587 Evaluate side-chains 20 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.100 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 63 optimal weight: 10.0000 chunk 133 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 2 optimal weight: 0.0010 chunk 199 optimal weight: 0.0980 chunk 214 optimal weight: 4.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.111433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095428 restraints weight = 21180.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100213 restraints weight = 10166.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.103404 restraints weight = 5779.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.105561 restraints weight = 3631.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.107058 restraints weight = 2416.378| |-----------------------------------------------------------------------------| r_work (final): 0.3651 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.153585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.145742 restraints weight = 19442.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.147589 restraints weight = 9265.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.148671 restraints weight = 4877.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.149306 restraints weight = 2826.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.149671 restraints weight = 1809.249| |-----------------------------------------------------------------------------| r_work (final): 0.4022 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.077712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.067604 restraints weight = 25722.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.070850 restraints weight = 12160.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.072916 restraints weight = 6561.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.074307 restraints weight = 3925.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.075243 restraints weight = 2475.363| |-----------------------------------------------------------------------------| r_work (final): 0.3717 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.073888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.069173 restraints weight = 379.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.070087 restraints weight = 233.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.070727 restraints weight = 172.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.071288 restraints weight = 136.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.071689 restraints weight = 108.617| |-----------------------------------------------------------------------------| r_work (final): 0.3051 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.048896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2336 r_free = 0.2336 target = 0.048580 restraints weight = 289.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.048793 restraints weight = 48.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.048865 restraints weight = 13.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.048871 restraints weight = 4.373 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.048866 restraints weight = 1.444 | |-----------------------------------------------------------------------------| r_work (final): 0.2335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 17997 Z= 0.149 Angle : 0.666 13.296 24459 Z= 0.353 Chirality : 0.042 0.174 2694 Planarity : 0.004 0.038 3132 Dihedral : 6.444 29.858 3075 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % 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: -2.51 (0.16), residues: 2172 helix: 1.29 (0.28), residues: 345 sheet: -1.74 (0.21), residues: 531 loop : -2.61 (0.14), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 576 TYR 0.027 0.002 TYR G 33 PHE 0.015 0.001 PHE I 100 TRP 0.011 0.001 TRP G 36 HIS 0.008 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (17943) covalent geometry : angle 0.64630 / 0.35 (24318) SS BOND : bond 0.03617 / 2.15 ( 21) SS BOND : angle 3.25819 / 1.98 ( 42) hydrogen bonds : bond 0.04470 / 2.89 ( 672) hydrogen bonds : angle 6.10433 / 4.21 ( 1926) link_BETA1-4 : bond 0.00398 / 0.22 ( 9) link_BETA1-4 : angle 1.34428 / 0.78 ( 27) link_NAG-ASN : bond 0.00265 / 0.18 ( 24) link_NAG-ASN : angle 1.69212 / 1.09 ( 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 65 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.146 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: A 103 GLU cc_start: 0.8327 (pt0) cc_final: 0.7776 (tt0) REVERT: A 171 ASN cc_start: 0.8724 (p0) cc_final: 0.8433 (t0) REVERT: A 208 HIS cc_start: 0.9141 (m90) cc_final: 0.8830 (m-70) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.1042 time to fit residues: 8.4498 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 43 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.079 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: D 568 LYS cc_start: 0.7845 (tptp) cc_final: 0.7045 (mmtm) REVERT: D 570 PHE cc_start: 0.7630 (m-10) cc_final: 0.6547 (m-10) REVERT: D 583 LYS cc_start: 0.6705 (tttt) cc_final: 0.6157 (ttmt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0836 time to fit residues: 4.2146 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 : 0.066 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 : 0.062 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: I 155 ASN cc_start: 0.9218 (p0) cc_final: 0.8964 (p0) REVERT: I 160 HIS cc_start: 0.8380 (m-70) cc_final: 0.7709 (m-70) REVERT: I 207 MET cc_start: 0.8706 (mpp) cc_final: 0.8112 (mpp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1078 time to fit residues: 3.3539 Evaluate side-chains 21 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.096 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 51 optimal weight: 0.0370 chunk 65 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 196 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 546 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.110102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.093965 restraints weight = 24216.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.098754 restraints weight = 11302.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.102032 restraints weight = 6346.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.104274 restraints weight = 3951.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.105685 restraints weight = 2636.036| |-----------------------------------------------------------------------------| r_work (final): 0.3683 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.127163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.118157 restraints weight = 16458.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.121171 restraints weight = 8301.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.123170 restraints weight = 4544.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.124385 restraints weight = 2619.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.124985 restraints weight = 1600.756| |-----------------------------------------------------------------------------| r_work (final): 0.4081 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.081523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.071762 restraints weight = 21950.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.074892 restraints weight = 10202.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.076902 restraints weight = 5488.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.078210 restraints weight = 3266.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.079159 restraints weight = 2087.346| |-----------------------------------------------------------------------------| r_work (final): 0.3713 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.073804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.069475 restraints weight = 363.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.070380 restraints weight = 213.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.071053 restraints weight = 151.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.071543 restraints weight = 117.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.071882 restraints weight = 92.848| |-----------------------------------------------------------------------------| r_work (final): 0.3057 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2238 r_free = 0.2238 target = 0.044773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2233 r_free = 0.2233 target = 0.044513 restraints weight = 241.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2227 r_free = 0.2227 target = 0.044706 restraints weight = 37.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2226 r_free = 0.2226 target = 0.044739 restraints weight = 9.996 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2225 r_free = 0.2225 target = 0.044747 restraints weight = 2.894 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2225 r_free = 0.2225 target = 0.044749 restraints weight = 0.866 | |-----------------------------------------------------------------------------| r_work (final): 0.2238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 17997 Z= 0.189 Angle : 0.691 12.338 24459 Z= 0.370 Chirality : 0.042 0.319 2694 Planarity : 0.005 0.084 3132 Dihedral : 6.432 29.258 3075 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.17), residues: 2172 helix: 1.29 (0.29), residues: 345 sheet: -1.88 (0.21), residues: 552 loop : -2.50 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 211 TYR 0.042 0.002 TYR D 524 PHE 0.013 0.001 PHE D 610 TRP 0.009 0.001 TRP H 36 HIS 0.005 0.001 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (17943) covalent geometry : angle 0.67618 / 0.37 (24318) SS BOND : bond 0.04757 / 2.90 ( 21) SS BOND : angle 2.65341 / 1.57 ( 42) hydrogen bonds : bond 0.04652 / 3.03 ( 672) hydrogen bonds : angle 6.42125 / 4.47 ( 1926) link_BETA1-4 : bond 0.00401 / 0.21 ( 9) link_BETA1-4 : angle 1.39285 / 0.80 ( 27) link_NAG-ASN : bond 0.00275 / 0.18 ( 24) link_NAG-ASN : angle 1.66737 / 1.07 ( 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 67 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 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: symmetry clash revert: symmetry clash REVERT: E 39 ASP cc_start: 0.8891 (p0) cc_final: 0.8566 (p0) REVERT: E 103 GLU cc_start: 0.8382 (pt0) cc_final: 0.7575 (tt0) REVERT: E 171 ASN cc_start: 0.8998 (p0) cc_final: 0.8682 (t0) REVERT: E 199 ASN cc_start: 0.9383 (p0) cc_final: 0.8981 (p0) REVERT: E 209 TYR cc_start: 0.8984 (t80) cc_final: 0.8764 (t80) REVERT: E 233 TYR cc_start: 0.8411 (m-80) cc_final: 0.8182 (m-80) REVERT: E 309 TYR cc_start: 0.7587 (t80) cc_final: 0.7259 (t80) REVERT: E 317 MET cc_start: 0.8698 (tpp) cc_final: 0.8410 (tpp) outliers start: 1 outliers final: 1 residues processed: 67 average time/residue: 0.0869 time to fit residues: 7.5366 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 : 0.143 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 : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 568 LYS cc_start: 0.7826 (tptp) cc_final: 0.6884 (mmtm) REVERT: D 570 PHE cc_start: 0.7765 (m-10) cc_final: 0.6784 (m-10) REVERT: D 583 LYS cc_start: 0.6855 (tttt) cc_final: 0.6170 (ttmt) REVERT: D 594 TYR cc_start: 0.7613 (t80) cc_final: 0.7405 (t80) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0830 time to fit residues: 4.1895 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 : 0.079 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 : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 155 ASN cc_start: 0.9242 (p0) cc_final: 0.9003 (p0) REVERT: I 207 MET cc_start: 0.8754 (mpp) cc_final: 0.8162 (mpp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1007 time to fit residues: 3.2752 Evaluate side-chains 20 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 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: 0.0009 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 28 optimal weight: 5.9990 chunk 115 optimal weight: 0.0770 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 72 optimal weight: 0.1980 chunk 79 optimal weight: 4.9990 chunk 186 optimal weight: 0.5980 chunk 209 optimal weight: 10.0000 chunk 112 optimal weight: 0.0970 chunk 183 optimal weight: 10.0000 overall best weight: 1.1938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.112480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.095731 restraints weight = 23914.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.100532 restraints weight = 11238.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103851 restraints weight = 6380.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.105993 restraints weight = 4008.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.107599 restraints weight = 2741.973| |-----------------------------------------------------------------------------| r_work (final): 0.3706 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.127009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.118002 restraints weight = 16668.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.121268 restraints weight = 8321.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.123068 restraints weight = 4442.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.124278 restraints weight = 2611.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.125016 restraints weight = 1615.564| |-----------------------------------------------------------------------------| r_work (final): 0.3831 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.081481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.071856 restraints weight = 21529.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.074894 restraints weight = 10146.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.076839 restraints weight = 5513.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.078120 restraints weight = 3315.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.078854 restraints weight = 2139.350| |-----------------------------------------------------------------------------| r_work (final): 0.3711 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.073881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.069714 restraints weight = 420.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.070767 restraints weight = 237.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.071475 restraints weight = 159.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.071970 restraints weight = 116.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072377 restraints weight = 87.810| |-----------------------------------------------------------------------------| r_work (final): 0.3084 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.062419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.057609 restraints weight = 720.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.057911 restraints weight = 574.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.058164 restraints weight = 504.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.058202 restraints weight = 457.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.058395 restraints weight = 450.278| |-----------------------------------------------------------------------------| r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.6557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 17997 Z= 0.155 Angle : 0.631 9.350 24459 Z= 0.340 Chirality : 0.042 0.164 2694 Planarity : 0.004 0.037 3132 Dihedral : 6.204 28.263 3075 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.17), residues: 2172 helix: 1.34 (0.29), residues: 345 sheet: -1.81 (0.21), residues: 546 loop : -2.44 (0.15), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 211 TYR 0.025 0.002 TYR G 33 PHE 0.012 0.001 PHE B 610 TRP 0.009 0.001 TRP I 36 HIS 0.003 0.001 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (17943) covalent geometry : angle 0.61689 / 0.34 (24318) SS BOND : bond 0.04478 / 2.78 ( 21) SS BOND : angle 2.57464 / 1.55 ( 42) hydrogen bonds : bond 0.04536 / 2.92 ( 672) hydrogen bonds : angle 6.23601 / 4.34 ( 1926) link_BETA1-4 : bond 0.00224 / 0.12 ( 9) link_BETA1-4 : angle 1.16789 / 0.68 ( 27) link_NAG-ASN : bond 0.00250 / 0.17 ( 24) link_NAG-ASN : angle 1.55947 / 0.99 ( 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 59 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 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 90 GLU cc_start: 0.7674 (tt0) cc_final: 0.7334 (tm-30) REVERT: A 103 GLU cc_start: 0.8326 (pt0) cc_final: 0.7696 (tt0) REVERT: A 151 LEU cc_start: 0.9039 (mt) cc_final: 0.8813 (mt) REVERT: A 171 ASN cc_start: 0.8789 (p0) cc_final: 0.8500 (t0) REVERT: A 208 HIS cc_start: 0.9141 (m90) cc_final: 0.8820 (m-70) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.0668 time to fit residues: 5.4624 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 : 0.139 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 : 0.077 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: D 568 LYS cc_start: 0.7800 (tptp) cc_final: 0.6932 (mmtm) REVERT: D 570 PHE cc_start: 0.7706 (m-10) cc_final: 0.6759 (m-10) REVERT: D 583 LYS cc_start: 0.6780 (tttt) cc_final: 0.6171 (ttmt) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0712 time to fit residues: 3.5967 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 : 0.078 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 : 0.095 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: symmetry clash revert: symmetry clash REVERT: I 155 ASN cc_start: 0.9190 (p0) cc_final: 0.8957 (p0) REVERT: I 195 SER cc_start: 0.8866 (t) cc_final: 0.8324 (m) REVERT: I 207 MET cc_start: 0.8700 (mpp) cc_final: 0.8115 (mpp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1030 time to fit residues: 3.3510 Evaluate side-chains 20 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.090 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 116 optimal weight: 0.4980 chunk 134 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 79 optimal weight: 0.0870 chunk 152 optimal weight: 7.9990 chunk 100 optimal weight: 0.0050 chunk 147 optimal weight: 0.4980 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 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 = 0.3775 r_free = 0.3775 target = 0.111747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.095860 restraints weight = 24342.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100689 restraints weight = 11263.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.103889 restraints weight = 6291.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106098 restraints weight = 3905.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107533 restraints weight = 2582.396| |-----------------------------------------------------------------------------| r_work (final): 0.3696 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.152857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.144452 restraints weight = 20105.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.146265 restraints weight = 9496.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.147287 restraints weight = 4955.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.147745 restraints weight = 2889.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.148138 restraints weight = 2097.289| |-----------------------------------------------------------------------------| r_work (final): 0.4011 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.082187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.072780 restraints weight = 20401.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.075932 restraints weight = 9325.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.077915 restraints weight = 4896.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.079206 restraints weight = 2836.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.080098 restraints weight = 1762.097| |-----------------------------------------------------------------------------| r_work (final): 0.3737 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.070058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.067833 restraints weight = 320.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068708 restraints weight = 139.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.069099 restraints weight = 71.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.069422 restraints weight = 42.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.069630 restraints weight = 26.486| |-----------------------------------------------------------------------------| r_work (final): 0.3012 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2232 r_free = 0.2232 target = 0.045924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2234 r_free = 0.2234 target = 0.045660 restraints weight = 261.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2227 r_free = 0.2227 target = 0.045812 restraints weight = 35.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2226 r_free = 0.2226 target = 0.045866 restraints weight = 8.222 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2226 r_free = 0.2226 target = 0.045879 restraints weight = 2.099 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2226 r_free = 0.2226 target = 0.045880 restraints weight = 0.559 | |-----------------------------------------------------------------------------| r_work (final): 0.2231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 17997 Z= 0.141 Angle : 0.632 9.031 24459 Z= 0.339 Chirality : 0.043 0.175 2694 Planarity : 0.004 0.041 3132 Dihedral : 5.987 26.583 3075 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % 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: -2.20 (0.17), residues: 2172 helix: 1.36 (0.29), residues: 351 sheet: -1.47 (0.22), residues: 480 loop : -2.37 (0.14), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 211 TYR 0.026 0.002 TYR G 32 PHE 0.013 0.001 PHE F 610 TRP 0.011 0.001 TRP G 36 HIS 0.005 0.001 HIS F 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (17943) covalent geometry : angle 0.61866 / 0.33 (24318) SS BOND : bond 0.04447 / 2.77 ( 21) SS BOND : angle 2.51124 / 1.53 ( 42) hydrogen bonds : bond 0.04341 / 2.80 ( 672) hydrogen bonds : angle 6.00579 / 4.18 ( 1926) link_BETA1-4 : bond 0.00399 / 0.22 ( 9) link_BETA1-4 : angle 1.18984 / 0.70 ( 27) link_NAG-ASN : bond 0.00237 / 0.15 ( 24) link_NAG-ASN : angle 1.43569 / 0.91 ( 72) =============================================================================== Job complete usr+sys time: 2613.88 seconds wall clock time: 46 minutes 11.54 seconds (2771.54 seconds total)