Starting phenix.real_space_refine on Sat Sep 12 01:20:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hjr_0237/09_2026/6hjr_0237.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hjr_0237/09_2026/6hjr_0237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6hjr_0237/09_2026/6hjr_0237.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hjr_0237/09_2026/6hjr_0237.cif" model { file = "/net/cci-nas-00/data/ceres_data/6hjr_0237/09_2026/6hjr_0237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hjr_0237/09_2026/6hjr_0237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hjr_0237/09_2026/6hjr_0237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hjr_0237/09_2026/6hjr_0237.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.205 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 7856 2.51 5 N 2116 2.21 5 O 2556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12579 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 17, 'TRANS': 305} Chain: "B" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1553 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 201} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 17, 'TRANS': 305} Chain: "D" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1553 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 201} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 17, 'TRANS': 305} Chain: "F" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1554 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 201} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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 chiralities: 3 Chain: "I" 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 chiralities: 2 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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 chiralities: 3 Chain: "L" 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 chiralities: 2 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 chiralities: 2 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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 chiralities: 3 Chain: "P" 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 chiralities: 2 Chain: "A" 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 chiralities: 2 Chain: "C" 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 chiralities: 1 Chain: "E" 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 chiralities: 2 Time building chain proxies: 2.34, per 1000 atoms: 0.19 Number of scatterers: 12579 At special positions: 0 Unit cell: (87.318, 87.318, 187.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2556 8.00 N 2116 7.00 C 7856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.02 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 144 " - pdb=" SG CYS B 148 " distance=2.02 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.02 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.02 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 144 " - pdb=" SG CYS D 148 " distance=2.02 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 137 " distance=2.02 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS E 278 " distance=2.02 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.02 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.02 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.02 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " " NAG N 1 " - " FUC N 3 " NAG-ASN " NAG A 401 " - " ASN A 15 " " NAG A 408 " - " ASN A 290 " " NAG C 401 " - " ASN C 15 " " NAG E 401 " - " ASN E 15 " " NAG E 408 " - " ASN E 290 " " NAG G 1 " - " ASN A 27 " " NAG H 1 " - " ASN A 91 " " NAG I 1 " - " ASN B 154 " " NAG J 1 " - " ASN C 27 " " NAG K 1 " - " ASN C 91 " " NAG L 1 " - " ASN C 290 " " NAG M 1 " - " ASN D 154 " " NAG N 1 " - " ASN E 27 " " NAG O 1 " - " ASN E 91 " " NAG P 1 " - " ASN F 154 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 535.4 milliseconds 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 31 sheets defined 28.7% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.635A pdb=" N ASP A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.553A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.731A pdb=" N GLN B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.657A pdb=" N SER B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.618A pdb=" N THR B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.701A pdb=" N ASP C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 110 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 59 removed outlier: 3.705A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 125 removed outlier: 3.554A pdb=" N GLN D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.748A pdb=" N MET D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 175 Processing helix chain 'D' and resid 186 through 202 removed outlier: 4.202A pdb=" N THR D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL D 193 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 194 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 101 through 110 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'F' and resid 37 through 59 removed outlier: 3.797A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN F 42 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 125 Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.879A pdb=" N MET F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 172 removed outlier: 3.804A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER F 166 " --> pdb=" O TYR F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 202 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.792A pdb=" N LEU A 46 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N CYS A 278 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 54 through 55 removed outlier: 7.188A pdb=" N LEU A 54 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.957A pdb=" N GLU A 98 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N TRP A 234 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 118 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 170 removed outlier: 3.950A pdb=" N ASN A 170 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP A 241 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB3, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.589A pdb=" N CYS C 8 " --> pdb=" O HIS D 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB6, first strand: chain 'C' and resid 46 through 49 removed outlier: 8.118A pdb=" N LEU C 46 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR C 280 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER C 48 " --> pdb=" O THR C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.918A pdb=" N LEU C 54 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 97 through 99 removed outlier: 5.183A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 118 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AC1, first strand: chain 'C' and resid 164 through 170 removed outlier: 4.075A pdb=" N ASN C 170 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP C 241 " --> pdb=" O ASN C 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AC3, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AC4, first strand: chain 'E' and resid 7 through 11 removed outlier: 3.623A pdb=" N CYS E 8 " --> pdb=" O HIS F 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 35 " --> pdb=" O TYR F 24 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AC6, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AC7, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AC8, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.851A pdb=" N LEU E 46 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N CYS E 278 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.812A pdb=" N LEU E 54 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 97 through 99 removed outlier: 6.962A pdb=" N GLU E 98 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N TRP E 234 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AD3, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD4, first strand: chain 'E' and resid 164 through 170 removed outlier: 4.294A pdb=" N ASN E 170 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP E 241 " --> pdb=" O ASN E 170 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1239 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: 1.65 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2140 1.31 - 1.44: 3600 1.44 - 1.56: 7046 1.56 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 12852 Sorted by residual: bond pdb=" N ILE F 189 " pdb=" CA ILE F 189 " ideal model delta sigma weight residual 1.456 1.485 -0.029 9.50e-03 1.11e+04 9.14e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.37e+00 bond pdb=" CA ILE F 189 " pdb=" CB ILE F 189 " ideal model delta sigma weight residual 1.543 1.508 0.035 1.24e-02 6.50e+03 7.84e+00 bond pdb=" N LEU F 187 " pdb=" CA LEU F 187 " ideal model delta sigma weight residual 1.458 1.484 -0.025 1.08e-02 8.57e+03 5.54e+00 bond pdb=" C1 FUC G 3 " pdb=" O5 FUC G 3 " ideal model delta sigma weight residual 1.400 1.447 -0.047 2.00e-02 2.50e+03 5.45e+00 ... (remaining 12847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 16292 2.04 - 4.09: 960 4.09 - 6.13: 136 6.13 - 8.17: 52 8.17 - 10.21: 13 Bond angle restraints: 17453 Sorted by residual: angle pdb=" N VAL F 176 " pdb=" CA VAL F 176 " pdb=" C VAL F 176 " ideal model delta sigma weight residual 113.20 106.86 6.34 9.60e-01 1.09e+00 4.37e+01 angle pdb=" CA ILE F 189 " pdb=" C ILE F 189 " pdb=" N TYR F 190 " ideal model delta sigma weight residual 119.31 112.20 7.11 1.15e+00 7.56e-01 3.82e+01 angle pdb=" N LEU D 187 " pdb=" CA LEU D 187 " pdb=" C LEU D 187 " ideal model delta sigma weight residual 111.28 117.75 -6.47 1.09e+00 8.42e-01 3.52e+01 angle pdb=" N TYR F 190 " pdb=" CA TYR F 190 " pdb=" C TYR F 190 " ideal model delta sigma weight residual 111.02 103.83 7.19 1.22e+00 6.72e-01 3.47e+01 angle pdb=" N ILE F 189 " pdb=" CA ILE F 189 " pdb=" C ILE F 189 " ideal model delta sigma weight residual 113.53 108.18 5.35 9.80e-01 1.04e+00 2.98e+01 ... (remaining 17448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 6837 15.87 - 31.74: 444 31.74 - 47.60: 97 47.60 - 63.47: 6 63.47 - 79.34: 6 Dihedral angle restraints: 7390 sinusoidal: 2833 harmonic: 4557 Sorted by residual: dihedral pdb=" CA PRO C 307 " pdb=" C PRO C 307 " pdb=" N LYS C 308 " pdb=" CA LYS C 308 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ILE D 18 " pdb=" C ILE D 18 " pdb=" N ASP D 19 " pdb=" CA ASP D 19 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual 93.00 50.12 42.88 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 7387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1645 0.082 - 0.164: 306 0.164 - 0.246: 22 0.246 - 0.328: 7 0.328 - 0.410: 5 Chirality restraints: 1985 Sorted by residual: chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 15 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C2 NAG P 2 " pdb=" C1 NAG P 2 " pdb=" C3 NAG P 2 " pdb=" N2 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.09 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C2 NAG M 2 " pdb=" C1 NAG M 2 " pdb=" C3 NAG M 2 " pdb=" N2 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 1982 not shown) Planarity restraints: 2254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 7 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ILE C 7 " -0.066 2.00e-02 2.50e+03 pdb=" O ILE C 7 " 0.025 2.00e-02 2.50e+03 pdb=" N CYS C 8 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 248 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C THR E 248 " -0.064 2.00e-02 2.50e+03 pdb=" O THR E 248 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY E 249 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 248 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C THR A 248 " -0.059 2.00e-02 2.50e+03 pdb=" O THR A 248 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY A 249 " 0.020 2.00e-02 2.50e+03 ... (remaining 2251 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1701 2.74 - 3.28: 12276 3.28 - 3.82: 21280 3.82 - 4.36: 22845 4.36 - 4.90: 39061 Nonbonded interactions: 97163 Sorted by model distance: nonbonded pdb=" OG1 THR A 6 " pdb=" OE1 GLN B 27 " model vdw 2.204 3.040 nonbonded pdb=" CH2 TRP E 80 " pdb=" CZ PHE E 115 " model vdw 2.227 3.640 nonbonded pdb=" OG SER A 207 " pdb=" OD1 ASP A 241 " model vdw 2.247 3.040 nonbonded pdb=" O TYR D 141 " pdb=" ND2 ASN D 169 " model vdw 2.249 3.120 nonbonded pdb=" O LYS C 157 " pdb=" OG SER C 160 " model vdw 2.250 3.040 ... (remaining 97158 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 401) selection = chain 'C' selection = (chain 'E' and resid 5 through 401) } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'F' and (resid 1 through 179 or (resid 180 through 181 and (name N or nam \ e CA or name C or name O or name CB )) or resid 182 through 203)) } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.000 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 12901 Z= 0.447 Angle : 1.156 11.290 17582 Z= 0.607 Chirality : 0.066 0.410 1985 Planarity : 0.007 0.054 2239 Dihedral : 11.242 79.340 4426 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.60 % Favored : 89.21 % Rotamer: Outliers : 0.70 % Allowed : 5.81 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.17), residues: 1566 helix: -0.68 (0.21), residues: 415 sheet: -1.76 (0.37), residues: 159 loop : -3.24 (0.15), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 106 TYR 0.044 0.003 TYR C 195 PHE 0.037 0.004 PHE D 140 TRP 0.046 0.005 TRP A 255 HIS 0.022 0.004 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.45 (12852) covalent geometry : angle 1.12941 / 0.60 (17453) SS BOND : bond 0.00788 / 0.49 ( 18) SS BOND : angle 1.68776 / 1.03 ( 36) hydrogen bonds : bond 0.18649 / 12.75 ( 444) hydrogen bonds : angle 6.74992 / 4.66 ( 1239) link_BETA1-4 : bond 0.00715 / 0.46 ( 13) link_BETA1-4 : angle 2.34016 / 1.52 ( 39) link_BETA1-6 : bond 0.00584 / 0.30 ( 3) link_BETA1-6 : angle 2.17037 / 1.87 ( 9) link_NAG-ASN : bond 0.01111 / 0.66 ( 15) link_NAG-ASN : angle 4.40235 / 2.70 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.540 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: A 115 PHE cc_start: 0.8658 (m-10) cc_final: 0.8222 (m-80) REVERT: B 62 GLN cc_start: 0.9129 (pt0) cc_final: 0.8716 (pm20) REVERT: C 211 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7648 (mmm-85) REVERT: C 251 LEU cc_start: 0.9512 (tp) cc_final: 0.9114 (tt) REVERT: D 94 TYR cc_start: 0.9635 (t80) cc_final: 0.9351 (t80) REVERT: D 149 MET cc_start: 0.9240 (mmp) cc_final: 0.8951 (mmm) REVERT: F 62 GLN cc_start: 0.9184 (pt0) cc_final: 0.8627 (pm20) outliers start: 9 outliers final: 0 residues processed: 105 average time/residue: 0.1222 time to fit residues: 18.5427 Evaluate side-chains 42 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 192 GLN A 261 ASN A 286 HIS C 108 GLN C 130 HIS C 286 HIS E 32 HIS E 108 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.034701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.026584 restraints weight = 95447.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.027494 restraints weight = 55571.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.028168 restraints weight = 38424.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.028650 restraints weight = 29215.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.028983 restraints weight = 23801.629| |-----------------------------------------------------------------------------| r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12901 Z= 0.146 Angle : 0.705 9.823 17582 Z= 0.357 Chirality : 0.045 0.261 1985 Planarity : 0.004 0.040 2239 Dihedral : 6.037 24.826 1695 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.79 % Favored : 92.08 % Rotamer: Outliers : 0.15 % Allowed : 1.24 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.23 (0.19), residues: 1566 helix: 1.54 (0.25), residues: 397 sheet: -1.81 (0.32), residues: 204 loop : -2.93 (0.16), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 106 TYR 0.019 0.002 TYR C 195 PHE 0.037 0.002 PHE B 140 TRP 0.017 0.002 TRP D 92 HIS 0.005 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (12852) covalent geometry : angle 0.68837 / 0.35 (17453) SS BOND : bond 0.00544 / 0.30 ( 18) SS BOND : angle 1.50778 / 0.94 ( 36) hydrogen bonds : bond 0.06905 / 4.68 ( 444) hydrogen bonds : angle 5.15142 / 3.53 ( 1239) link_BETA1-4 : bond 0.00423 / 0.27 ( 13) link_BETA1-4 : angle 1.38037 / 0.91 ( 39) link_BETA1-6 : bond 0.00468 / 0.24 ( 3) link_BETA1-6 : angle 1.39477 / 0.94 ( 9) link_NAG-ASN : bond 0.00291 / 0.16 ( 15) link_NAG-ASN : angle 2.56061 / 1.50 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8599 (tmm) cc_final: 0.8367 (tmm) REVERT: B 62 GLN cc_start: 0.9039 (pt0) cc_final: 0.8538 (pm20) REVERT: B 109 ASP cc_start: 0.9117 (p0) cc_final: 0.8734 (m-30) REVERT: C 7 ILE cc_start: 0.9536 (OUTLIER) cc_final: 0.9318 (mp) REVERT: C 211 ARG cc_start: 0.8015 (ttm170) cc_final: 0.7717 (mmm-85) REVERT: C 251 LEU cc_start: 0.9443 (tp) cc_final: 0.9062 (tt) REVERT: C 317 MET cc_start: 0.8199 (tmm) cc_final: 0.7988 (tmm) REVERT: D 120 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8408 (mp0) REVERT: D 133 ILE cc_start: 0.9666 (pt) cc_final: 0.9103 (mm) REVERT: E 239 GLN cc_start: 0.9687 (pm20) cc_final: 0.8941 (pm20) REVERT: E 317 MET cc_start: 0.8976 (tmm) cc_final: 0.8403 (tmm) REVERT: F 62 GLN cc_start: 0.9081 (pt0) cc_final: 0.8414 (pm20) outliers start: 2 outliers final: 0 residues processed: 75 average time/residue: 0.1202 time to fit residues: 13.5095 Evaluate side-chains 43 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 17 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 130 optimal weight: 0.2980 chunk 97 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS C 130 HIS C 226 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.034785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.026672 restraints weight = 96521.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.027607 restraints weight = 55840.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.028276 restraints weight = 38533.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.028757 restraints weight = 29187.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.029107 restraints weight = 23714.918| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12901 Z= 0.141 Angle : 0.632 9.565 17582 Z= 0.319 Chirality : 0.044 0.244 1985 Planarity : 0.003 0.035 2239 Dihedral : 5.413 24.340 1695 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.24 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.20), residues: 1566 helix: 2.16 (0.25), residues: 392 sheet: -1.47 (0.32), residues: 207 loop : -2.71 (0.16), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 106 TYR 0.021 0.001 TYR F 190 PHE 0.018 0.002 PHE E 115 TRP 0.012 0.001 TRP D 92 HIS 0.005 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (12852) covalent geometry : angle 0.61877 / 0.32 (17453) SS BOND : bond 0.00448 / 0.27 ( 18) SS BOND : angle 1.19880 / 0.74 ( 36) hydrogen bonds : bond 0.06161 / 4.19 ( 444) hydrogen bonds : angle 4.79740 / 3.31 ( 1239) link_BETA1-4 : bond 0.00398 / 0.25 ( 13) link_BETA1-4 : angle 1.28139 / 0.84 ( 39) link_BETA1-6 : bond 0.00541 / 0.28 ( 3) link_BETA1-6 : angle 1.14163 / 0.80 ( 9) link_NAG-ASN : bond 0.00234 / 0.13 ( 15) link_NAG-ASN : angle 2.15395 / 1.24 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8787 (tmm) cc_final: 0.8367 (tmm) REVERT: B 62 GLN cc_start: 0.8958 (pt0) cc_final: 0.8452 (pm20) REVERT: B 109 ASP cc_start: 0.9103 (p0) cc_final: 0.8799 (m-30) REVERT: C 211 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7799 (mmm-85) REVERT: C 230 MET cc_start: 0.9192 (mmm) cc_final: 0.8820 (mmm) REVERT: C 317 MET cc_start: 0.8328 (tmm) cc_final: 0.8074 (tmm) REVERT: D 140 PHE cc_start: 0.8930 (m-80) cc_final: 0.8655 (m-80) REVERT: E 269 ILE cc_start: 0.9333 (mt) cc_final: 0.9047 (tt) REVERT: E 317 MET cc_start: 0.9022 (tmm) cc_final: 0.8382 (tmm) REVERT: F 62 GLN cc_start: 0.9064 (pt0) cc_final: 0.8376 (pm20) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1065 time to fit residues: 10.5221 Evaluate side-chains 41 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 72 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 HIS F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.034652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.026616 restraints weight = 96629.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.027530 restraints weight = 56153.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.028201 restraints weight = 38801.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.028672 restraints weight = 29286.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.029011 restraints weight = 23853.513| |-----------------------------------------------------------------------------| r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12901 Z= 0.141 Angle : 0.613 9.509 17582 Z= 0.310 Chirality : 0.043 0.238 1985 Planarity : 0.003 0.033 2239 Dihedral : 5.149 24.335 1695 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.37 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.20), residues: 1566 helix: 2.48 (0.26), residues: 393 sheet: -1.46 (0.32), residues: 219 loop : -2.59 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 149 TYR 0.019 0.001 TYR F 190 PHE 0.026 0.002 PHE C 115 TRP 0.029 0.001 TRP E 255 HIS 0.005 0.001 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (12852) covalent geometry : angle 0.60163 / 0.31 (17453) SS BOND : bond 0.00326 / 0.19 ( 18) SS BOND : angle 1.15585 / 0.71 ( 36) hydrogen bonds : bond 0.05689 / 3.89 ( 444) hydrogen bonds : angle 4.58388 / 3.15 ( 1239) link_BETA1-4 : bond 0.00362 / 0.23 ( 13) link_BETA1-4 : angle 1.23052 / 0.80 ( 39) link_BETA1-6 : bond 0.00460 / 0.23 ( 3) link_BETA1-6 : angle 1.12594 / 0.78 ( 9) link_NAG-ASN : bond 0.00250 / 0.15 ( 15) link_NAG-ASN : angle 1.99175 / 1.15 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8907 (tmm) cc_final: 0.8474 (tmm) REVERT: B 149 MET cc_start: 0.8986 (mmt) cc_final: 0.8749 (mmt) REVERT: C 211 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7843 (mmm-85) REVERT: C 230 MET cc_start: 0.9118 (mmm) cc_final: 0.8750 (mmm) REVERT: C 317 MET cc_start: 0.8425 (tmm) cc_final: 0.8106 (tmm) REVERT: D 140 PHE cc_start: 0.8994 (m-80) cc_final: 0.8363 (m-80) REVERT: E 269 ILE cc_start: 0.9314 (mt) cc_final: 0.9041 (tt) REVERT: E 317 MET cc_start: 0.9017 (tmm) cc_final: 0.8381 (tmm) REVERT: F 38 GLN cc_start: 0.9148 (pm20) cc_final: 0.8940 (pm20) REVERT: F 62 GLN cc_start: 0.9035 (pt0) cc_final: 0.8333 (pm20) REVERT: F 109 ASP cc_start: 0.8850 (m-30) cc_final: 0.7912 (m-30) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1215 time to fit residues: 10.4846 Evaluate side-chains 40 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 124 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 ASN F 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.033131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.025176 restraints weight = 99140.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.026063 restraints weight = 57323.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.026711 restraints weight = 39632.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.027177 restraints weight = 29959.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.027517 restraints weight = 24461.584| |-----------------------------------------------------------------------------| r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12901 Z= 0.289 Angle : 0.744 9.502 17582 Z= 0.374 Chirality : 0.045 0.231 1985 Planarity : 0.004 0.029 2239 Dihedral : 5.341 23.551 1695 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.60 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.20), residues: 1566 helix: 2.23 (0.26), residues: 398 sheet: -1.44 (0.33), residues: 213 loop : -2.68 (0.17), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 212 TYR 0.018 0.002 TYR E 209 PHE 0.016 0.003 PHE A 245 TRP 0.027 0.002 TRP E 255 HIS 0.009 0.002 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.29 (12852) covalent geometry : angle 0.73213 / 0.37 (17453) SS BOND : bond 0.00533 / 0.32 ( 18) SS BOND : angle 1.23168 / 0.76 ( 36) hydrogen bonds : bond 0.06122 / 4.17 ( 444) hydrogen bonds : angle 4.86157 / 3.33 ( 1239) link_BETA1-4 : bond 0.00408 / 0.22 ( 13) link_BETA1-4 : angle 1.36479 / 0.91 ( 39) link_BETA1-6 : bond 0.00589 / 0.31 ( 3) link_BETA1-6 : angle 1.22130 / 0.87 ( 9) link_NAG-ASN : bond 0.00579 / 0.36 ( 15) link_NAG-ASN : angle 2.29100 / 1.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8859 (mtp) cc_final: 0.8281 (mtm) REVERT: A 317 MET cc_start: 0.9012 (tmm) cc_final: 0.8526 (tmm) REVERT: B 109 ASP cc_start: 0.9073 (m-30) cc_final: 0.8696 (p0) REVERT: C 164 LEU cc_start: 0.9338 (tp) cc_final: 0.9113 (tp) REVERT: C 230 MET cc_start: 0.9127 (mmm) cc_final: 0.8731 (mmm) REVERT: C 317 MET cc_start: 0.8696 (tmm) cc_final: 0.8270 (tmm) REVERT: D 140 PHE cc_start: 0.9227 (m-80) cc_final: 0.8678 (m-80) REVERT: E 269 ILE cc_start: 0.9397 (mt) cc_final: 0.9152 (tt) REVERT: E 317 MET cc_start: 0.9131 (tmm) cc_final: 0.8442 (tmm) REVERT: F 62 GLN cc_start: 0.9054 (pt0) cc_final: 0.8314 (pm20) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1121 time to fit residues: 9.3890 Evaluate side-chains 39 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 49 optimal weight: 0.0040 chunk 146 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 283 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.034249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.026347 restraints weight = 95159.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.027288 restraints weight = 54642.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.027945 restraints weight = 37270.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.028433 restraints weight = 28100.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.028707 restraints weight = 22732.820| |-----------------------------------------------------------------------------| r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12901 Z= 0.122 Angle : 0.609 9.521 17582 Z= 0.306 Chirality : 0.043 0.239 1985 Planarity : 0.003 0.030 2239 Dihedral : 4.997 24.466 1695 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.34 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.21), residues: 1566 helix: 2.66 (0.26), residues: 397 sheet: -1.44 (0.32), residues: 219 loop : -2.49 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 229 TYR 0.018 0.001 TYR C 161 PHE 0.017 0.002 PHE E 115 TRP 0.028 0.002 TRP C 255 HIS 0.004 0.001 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (12852) covalent geometry : angle 0.59779 / 0.30 (17453) SS BOND : bond 0.00388 / 0.22 ( 18) SS BOND : angle 1.10013 / 0.68 ( 36) hydrogen bonds : bond 0.05722 / 3.90 ( 444) hydrogen bonds : angle 4.47358 / 3.04 ( 1239) link_BETA1-4 : bond 0.00416 / 0.26 ( 13) link_BETA1-4 : angle 1.19123 / 0.75 ( 39) link_BETA1-6 : bond 0.00562 / 0.29 ( 3) link_BETA1-6 : angle 1.08485 / 0.74 ( 9) link_NAG-ASN : bond 0.00242 / 0.14 ( 15) link_NAG-ASN : angle 1.92249 / 1.10 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8855 (mtp) cc_final: 0.8345 (mtm) REVERT: A 317 MET cc_start: 0.9012 (tmm) cc_final: 0.8424 (tmm) REVERT: B 27 GLN cc_start: 0.9199 (tm-30) cc_final: 0.8949 (tm-30) REVERT: B 109 ASP cc_start: 0.9049 (m-30) cc_final: 0.8645 (p0) REVERT: C 164 LEU cc_start: 0.9282 (tp) cc_final: 0.8880 (mt) REVERT: C 211 ARG cc_start: 0.8976 (ttm110) cc_final: 0.8202 (mmm-85) REVERT: C 230 MET cc_start: 0.9076 (mmm) cc_final: 0.8718 (mmm) REVERT: C 317 MET cc_start: 0.8631 (tmm) cc_final: 0.8178 (tmm) REVERT: D 140 PHE cc_start: 0.9133 (m-80) cc_final: 0.8568 (m-80) REVERT: E 269 ILE cc_start: 0.9335 (mt) cc_final: 0.9103 (tt) REVERT: E 317 MET cc_start: 0.9062 (tmm) cc_final: 0.8414 (tmm) REVERT: F 62 GLN cc_start: 0.9005 (pt0) cc_final: 0.8257 (pm20) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1173 time to fit residues: 10.5433 Evaluate side-chains 40 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.033970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.026013 restraints weight = 96725.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.026923 restraints weight = 55752.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.027583 restraints weight = 38389.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.028066 restraints weight = 29049.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.028420 restraints weight = 23548.624| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12901 Z= 0.166 Angle : 0.616 9.523 17582 Z= 0.311 Chirality : 0.043 0.239 1985 Planarity : 0.003 0.031 2239 Dihedral : 4.874 22.320 1695 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.88 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.21), residues: 1566 helix: 2.73 (0.26), residues: 397 sheet: -1.29 (0.34), residues: 204 loop : -2.39 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 211 TYR 0.015 0.001 TYR C 195 PHE 0.014 0.002 PHE A 115 TRP 0.023 0.002 TRP C 255 HIS 0.006 0.001 HIS E 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (12852) covalent geometry : angle 0.60580 / 0.31 (17453) SS BOND : bond 0.00384 / 0.22 ( 18) SS BOND : angle 1.06575 / 0.67 ( 36) hydrogen bonds : bond 0.05526 / 3.76 ( 444) hydrogen bonds : angle 4.49873 / 3.05 ( 1239) link_BETA1-4 : bond 0.00362 / 0.23 ( 13) link_BETA1-4 : angle 1.20998 / 0.79 ( 39) link_BETA1-6 : bond 0.00513 / 0.26 ( 3) link_BETA1-6 : angle 1.11676 / 0.79 ( 9) link_NAG-ASN : bond 0.00316 / 0.19 ( 15) link_NAG-ASN : angle 1.92530 / 1.10 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8895 (mtp) cc_final: 0.8371 (mtm) REVERT: A 317 MET cc_start: 0.9048 (tmm) cc_final: 0.8438 (tmm) REVERT: B 27 GLN cc_start: 0.9240 (tm-30) cc_final: 0.8962 (tm-30) REVERT: B 109 ASP cc_start: 0.9008 (m-30) cc_final: 0.8619 (p0) REVERT: B 149 MET cc_start: 0.8941 (mmt) cc_final: 0.8738 (mmt) REVERT: C 164 LEU cc_start: 0.9294 (tp) cc_final: 0.8882 (mt) REVERT: C 211 ARG cc_start: 0.8979 (ttm110) cc_final: 0.8281 (mmm-85) REVERT: C 230 MET cc_start: 0.9040 (mmm) cc_final: 0.8785 (mmm) REVERT: C 317 MET cc_start: 0.8720 (tmm) cc_final: 0.8307 (tmm) REVERT: D 140 PHE cc_start: 0.9270 (m-80) cc_final: 0.8746 (m-80) REVERT: E 269 ILE cc_start: 0.9377 (mt) cc_final: 0.9141 (tt) REVERT: E 317 MET cc_start: 0.9073 (tmm) cc_final: 0.8364 (tmm) REVERT: F 62 GLN cc_start: 0.8993 (pt0) cc_final: 0.8199 (pm20) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1200 time to fit residues: 10.6249 Evaluate side-chains 40 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 40.0000 chunk 133 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.033521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.025590 restraints weight = 96458.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.026473 restraints weight = 55917.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.027113 restraints weight = 38779.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.027581 restraints weight = 29366.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.027840 restraints weight = 23967.522| |-----------------------------------------------------------------------------| r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12901 Z= 0.211 Angle : 0.660 9.655 17582 Z= 0.330 Chirality : 0.044 0.243 1985 Planarity : 0.003 0.030 2239 Dihedral : 4.952 23.656 1695 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.39 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1566 helix: 2.60 (0.26), residues: 402 sheet: -1.38 (0.34), residues: 204 loop : -2.38 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 127 TYR 0.016 0.002 TYR C 195 PHE 0.014 0.002 PHE A 115 TRP 0.022 0.002 TRP E 255 HIS 0.006 0.002 HIS E 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (12852) covalent geometry : angle 0.64910 / 0.33 (17453) SS BOND : bond 0.00412 / 0.24 ( 18) SS BOND : angle 1.12348 / 0.70 ( 36) hydrogen bonds : bond 0.05662 / 3.87 ( 444) hydrogen bonds : angle 4.56683 / 3.11 ( 1239) link_BETA1-4 : bond 0.00357 / 0.21 ( 13) link_BETA1-4 : angle 1.24569 / 0.81 ( 39) link_BETA1-6 : bond 0.00488 / 0.25 ( 3) link_BETA1-6 : angle 1.13350 / 0.81 ( 9) link_NAG-ASN : bond 0.00412 / 0.26 ( 15) link_NAG-ASN : angle 1.99610 / 1.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8146 (ttm-80) REVERT: A 230 MET cc_start: 0.8862 (mtp) cc_final: 0.8337 (mtm) REVERT: A 317 MET cc_start: 0.9060 (tmm) cc_final: 0.8504 (tmm) REVERT: B 27 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8972 (tm-30) REVERT: B 109 ASP cc_start: 0.9011 (m-30) cc_final: 0.8633 (p0) REVERT: C 164 LEU cc_start: 0.9346 (tp) cc_final: 0.8923 (mt) REVERT: C 211 ARG cc_start: 0.8872 (ttm110) cc_final: 0.7984 (mmm-85) REVERT: C 230 MET cc_start: 0.9034 (mmm) cc_final: 0.8786 (mmm) REVERT: C 317 MET cc_start: 0.8783 (tmm) cc_final: 0.8332 (tmm) REVERT: D 140 PHE cc_start: 0.9285 (m-80) cc_final: 0.8838 (m-80) REVERT: E 115 PHE cc_start: 0.8474 (m-80) cc_final: 0.8272 (m-10) REVERT: E 269 ILE cc_start: 0.9367 (mt) cc_final: 0.9155 (tt) REVERT: E 317 MET cc_start: 0.9049 (tmm) cc_final: 0.8356 (tmm) REVERT: F 62 GLN cc_start: 0.9029 (pt0) cc_final: 0.8233 (pm20) REVERT: F 109 ASP cc_start: 0.8751 (m-30) cc_final: 0.8532 (m-30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1056 time to fit residues: 9.2505 Evaluate side-chains 42 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 56 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 142 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.033458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.025513 restraints weight = 97497.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.026398 restraints weight = 56400.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.027045 restraints weight = 39005.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.027522 restraints weight = 29617.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.027857 restraints weight = 24092.932| |-----------------------------------------------------------------------------| r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12901 Z= 0.205 Angle : 0.652 9.508 17582 Z= 0.327 Chirality : 0.044 0.246 1985 Planarity : 0.003 0.029 2239 Dihedral : 4.911 21.963 1695 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.00 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.21), residues: 1566 helix: 2.62 (0.26), residues: 405 sheet: -1.35 (0.34), residues: 204 loop : -2.37 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 127 TYR 0.016 0.002 TYR C 195 PHE 0.014 0.002 PHE B 63 TRP 0.022 0.002 TRP C 255 HIS 0.006 0.001 HIS E 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (12852) covalent geometry : angle 0.64088 / 0.32 (17453) SS BOND : bond 0.00375 / 0.22 ( 18) SS BOND : angle 1.31269 / 0.78 ( 36) hydrogen bonds : bond 0.05660 / 3.87 ( 444) hydrogen bonds : angle 4.54758 / 3.10 ( 1239) link_BETA1-4 : bond 0.00346 / 0.21 ( 13) link_BETA1-4 : angle 1.21912 / 0.79 ( 39) link_BETA1-6 : bond 0.00497 / 0.25 ( 3) link_BETA1-6 : angle 1.12264 / 0.79 ( 9) link_NAG-ASN : bond 0.00400 / 0.25 ( 15) link_NAG-ASN : angle 1.96998 / 1.15 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8169 (ttm-80) REVERT: A 230 MET cc_start: 0.8845 (mtp) cc_final: 0.8322 (mtm) REVERT: A 317 MET cc_start: 0.9067 (tmm) cc_final: 0.8508 (tmm) REVERT: B 27 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8966 (tm-30) REVERT: C 164 LEU cc_start: 0.9349 (tp) cc_final: 0.8918 (mt) REVERT: C 211 ARG cc_start: 0.8832 (ttm110) cc_final: 0.7867 (mmm-85) REVERT: C 230 MET cc_start: 0.9066 (mmm) cc_final: 0.8802 (mmm) REVERT: C 317 MET cc_start: 0.8841 (tmm) cc_final: 0.8445 (tmm) REVERT: D 140 PHE cc_start: 0.9287 (m-80) cc_final: 0.8912 (m-80) REVERT: E 115 PHE cc_start: 0.8380 (m-80) cc_final: 0.8115 (m-10) REVERT: E 269 ILE cc_start: 0.9368 (mt) cc_final: 0.9160 (tt) REVERT: E 317 MET cc_start: 0.9064 (tmm) cc_final: 0.8354 (tmm) REVERT: F 62 GLN cc_start: 0.9027 (pt0) cc_final: 0.8228 (pm20) REVERT: F 109 ASP cc_start: 0.8750 (m-30) cc_final: 0.8524 (m-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1132 time to fit residues: 9.5901 Evaluate side-chains 41 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 114 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 55 optimal weight: 0.0070 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN E 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.034349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.026374 restraints weight = 95752.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.027302 restraints weight = 54564.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.027970 restraints weight = 37188.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.028465 restraints weight = 27967.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.028776 restraints weight = 22691.521| |-----------------------------------------------------------------------------| r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12901 Z= 0.122 Angle : 0.602 9.539 17582 Z= 0.300 Chirality : 0.043 0.246 1985 Planarity : 0.003 0.030 2239 Dihedral : 4.686 22.302 1695 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.28 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.21), residues: 1566 helix: 2.83 (0.26), residues: 402 sheet: -1.20 (0.35), residues: 204 loop : -2.28 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 127 TYR 0.014 0.001 TYR F 190 PHE 0.015 0.002 PHE E 115 TRP 0.020 0.001 TRP C 255 HIS 0.004 0.001 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (12852) covalent geometry : angle 0.59187 / 0.30 (17453) SS BOND : bond 0.00304 / 0.18 ( 18) SS BOND : angle 1.22840 / 0.72 ( 36) hydrogen bonds : bond 0.05402 / 3.69 ( 444) hydrogen bonds : angle 4.35431 / 2.96 ( 1239) link_BETA1-4 : bond 0.00411 / 0.26 ( 13) link_BETA1-4 : angle 1.15021 / 0.74 ( 39) link_BETA1-6 : bond 0.00510 / 0.26 ( 3) link_BETA1-6 : angle 1.09521 / 0.74 ( 9) link_NAG-ASN : bond 0.00215 / 0.12 ( 15) link_NAG-ASN : angle 1.73347 / 0.99 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.8136 (ttm-80) REVERT: A 230 MET cc_start: 0.8829 (mtp) cc_final: 0.8303 (mtm) REVERT: A 317 MET cc_start: 0.9065 (tmm) cc_final: 0.8462 (tmm) REVERT: B 27 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8958 (tm-30) REVERT: C 164 LEU cc_start: 0.9283 (tp) cc_final: 0.8867 (mt) REVERT: C 211 ARG cc_start: 0.8871 (ttm110) cc_final: 0.8075 (mmm-85) REVERT: C 230 MET cc_start: 0.9116 (mmm) cc_final: 0.8855 (mmm) REVERT: C 317 MET cc_start: 0.8764 (tmm) cc_final: 0.8313 (tmm) REVERT: D 140 PHE cc_start: 0.9266 (m-80) cc_final: 0.8929 (m-80) REVERT: E 115 PHE cc_start: 0.8390 (m-80) cc_final: 0.8178 (m-10) REVERT: E 269 ILE cc_start: 0.9358 (mt) cc_final: 0.9151 (tt) REVERT: E 317 MET cc_start: 0.9033 (tmm) cc_final: 0.8401 (tmm) REVERT: F 62 GLN cc_start: 0.8974 (pt0) cc_final: 0.8211 (pm20) REVERT: F 109 ASP cc_start: 0.8694 (m-30) cc_final: 0.8456 (m-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1173 time to fit residues: 9.9262 Evaluate side-chains 41 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 85 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.034916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.026926 restraints weight = 94738.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.027895 restraints weight = 53759.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028603 restraints weight = 36018.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.029099 restraints weight = 26882.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.029401 restraints weight = 21770.435| |-----------------------------------------------------------------------------| r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12901 Z= 0.110 Angle : 0.581 9.542 17582 Z= 0.289 Chirality : 0.043 0.244 1985 Planarity : 0.003 0.030 2239 Dihedral : 4.492 21.000 1695 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.92 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.21), residues: 1566 helix: 2.96 (0.26), residues: 402 sheet: -1.07 (0.35), residues: 204 loop : -2.20 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 127 TYR 0.015 0.001 TYR F 190 PHE 0.028 0.001 PHE B 140 TRP 0.019 0.001 TRP C 255 HIS 0.004 0.001 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (12852) covalent geometry : angle 0.57147 / 0.29 (17453) SS BOND : bond 0.00279 / 0.17 ( 18) SS BOND : angle 1.17897 / 0.69 ( 36) hydrogen bonds : bond 0.05056 / 3.45 ( 444) hydrogen bonds : angle 4.27422 / 2.90 ( 1239) link_BETA1-4 : bond 0.00425 / 0.27 ( 13) link_BETA1-4 : angle 1.13087 / 0.73 ( 39) link_BETA1-6 : bond 0.00512 / 0.26 ( 3) link_BETA1-6 : angle 1.09153 / 0.74 ( 9) link_NAG-ASN : bond 0.00179 / 0.10 ( 15) link_NAG-ASN : angle 1.63291 / 0.93 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1642.63 seconds wall clock time: 29 minutes 40.44 seconds (1780.44 seconds total)