Starting phenix.real_space_refine on Thu Sep 18 01:06:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hjr_0237/09_2025/6hjr_0237.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hjr_0237/09_2025/6hjr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6hjr_0237/09_2025/6hjr_0237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hjr_0237/09_2025/6hjr_0237.map" model { file = "/net/cci-nas-00/data/ceres_data/6hjr_0237/09_2025/6hjr_0237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hjr_0237/09_2025/6hjr_0237.cif" } 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-2.0-5805/lib/python3.9/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.52, per 1000 atoms: 0.28 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: 1.23 Conformation dependent library (CDL) restraints added in 527.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.47 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: 1.95 Time building geometry restraints manager: 1.60 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 - 20.96: 7601 20.96 - 41.93: 326 41.93 - 62.89: 61 62.89 - 83.86: 23 83.86 - 104.82: 12 Dihedral angle restraints: 8023 sinusoidal: 3466 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 8020 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: 14.410 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.490 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 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 : 13.656 104.819 5059 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 aren 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 covalent geometry : bond 0.00943 (12852) covalent geometry : angle 1.12941 (17453) SS BOND : bond 0.00788 ( 18) SS BOND : angle 1.68776 ( 36) hydrogen bonds : bond 0.18649 ( 444) hydrogen bonds : angle 6.74992 ( 1239) link_BETA1-4 : bond 0.00715 ( 13) link_BETA1-4 : angle 2.34016 ( 39) link_BETA1-6 : bond 0.00584 ( 3) link_BETA1-6 : angle 2.17037 ( 9) link_NAG-ASN : bond 0.01111 ( 15) link_NAG-ASN : angle 4.40235 ( 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 : 0.509 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: 0.9241 (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: 0.1329 time to fit residues: 19.7675 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 : 0.522 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 E 283 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.034778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.026665 restraints weight = 94587.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.027583 restraints weight = 54664.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.028257 restraints weight = 37783.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.028740 restraints weight = 28647.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.029071 restraints weight = 23322.248| |-----------------------------------------------------------------------------| r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12901 Z= 0.147 Angle : 0.708 9.772 17582 Z= 0.356 Chirality : 0.046 0.248 1985 Planarity : 0.004 0.038 2239 Dihedral : 10.803 69.542 2328 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.73 % Favored : 92.15 % Rotamer: Outliers : 0.23 % Allowed : 1.16 % 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 aren not related in a simple way. whole: -2.20 (0.19), residues: 1566 helix: 1.56 (0.25), residues: 397 sheet: -1.78 (0.32), residues: 204 loop : -2.92 (0.16), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 106 TYR 0.020 0.002 TYR C 195 PHE 0.042 0.002 PHE B 140 TRP 0.017 0.002 TRP D 92 HIS 0.006 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00297 (12852) covalent geometry : angle 0.68953 (17453) SS BOND : bond 0.00557 ( 18) SS BOND : angle 1.35966 ( 36) hydrogen bonds : bond 0.06819 ( 444) hydrogen bonds : angle 5.13276 ( 1239) link_BETA1-4 : bond 0.00532 ( 13) link_BETA1-4 : angle 1.85885 ( 39) link_BETA1-6 : bond 0.00489 ( 3) link_BETA1-6 : angle 1.40180 ( 9) link_NAG-ASN : bond 0.00245 ( 15) link_NAG-ASN : angle 2.53089 ( 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 77 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8644 (tmm) cc_final: 0.8411 (tmm) REVERT: B 62 GLN cc_start: 0.9031 (pt0) cc_final: 0.8531 (pm20) REVERT: B 109 ASP cc_start: 0.9133 (p0) cc_final: 0.8782 (m-30) REVERT: C 7 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9281 (mp) REVERT: C 211 ARG cc_start: 0.8008 (ttm170) cc_final: 0.7706 (mmm-85) REVERT: C 251 LEU cc_start: 0.9443 (tp) cc_final: 0.9070 (tt) REVERT: C 317 MET cc_start: 0.8195 (tmm) cc_final: 0.7972 (tmm) REVERT: D 120 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8409 (mp0) REVERT: D 133 ILE cc_start: 0.9666 (pt) cc_final: 0.9097 (mm) REVERT: E 239 GLN cc_start: 0.9688 (pm20) cc_final: 0.8951 (pm20) REVERT: E 317 MET cc_start: 0.8992 (tmm) cc_final: 0.8459 (tmm) REVERT: F 62 GLN cc_start: 0.9068 (pt0) cc_final: 0.8438 (pm20) outliers start: 3 outliers final: 0 residues processed: 76 average time/residue: 0.1154 time to fit residues: 13.0369 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 : 0.489 ------------------------------------------------------------------------------- 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: 0.0170 chunk 95 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 113 optimal weight: 0.0070 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN C 130 HIS F 111 HIS ** 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 = 0.2805 r_free = 0.2805 target = 0.035482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.027311 restraints weight = 95345.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.028255 restraints weight = 55222.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.028942 restraints weight = 37994.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.029421 restraints weight = 28654.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.029695 restraints weight = 23349.181| |-----------------------------------------------------------------------------| r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12901 Z= 0.120 Angle : 0.632 9.687 17582 Z= 0.316 Chirality : 0.045 0.252 1985 Planarity : 0.003 0.035 2239 Dihedral : 8.644 58.681 2328 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.47 % Favored : 92.40 % Rotamer: Outliers : 0.08 % Allowed : 1.86 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.69 (0.20), residues: 1566 helix: 2.16 (0.25), residues: 391 sheet: -1.49 (0.32), residues: 219 loop : -2.65 (0.17), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 106 TYR 0.022 0.001 TYR F 190 PHE 0.019 0.002 PHE E 115 TRP 0.013 0.001 TRP F 92 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00233 (12852) covalent geometry : angle 0.61762 (17453) SS BOND : bond 0.00440 ( 18) SS BOND : angle 1.22035 ( 36) hydrogen bonds : bond 0.05955 ( 444) hydrogen bonds : angle 4.64906 ( 1239) link_BETA1-4 : bond 0.00563 ( 13) link_BETA1-4 : angle 1.65084 ( 39) link_BETA1-6 : bond 0.00550 ( 3) link_BETA1-6 : angle 1.13214 ( 9) link_NAG-ASN : bond 0.00182 ( 15) link_NAG-ASN : angle 2.04702 ( 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 69 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8828 (tmm) cc_final: 0.8462 (tmm) REVERT: B 109 ASP cc_start: 0.9031 (p0) cc_final: 0.8804 (m-30) REVERT: B 140 PHE cc_start: 0.8663 (m-80) cc_final: 0.8393 (m-80) REVERT: C 211 ARG cc_start: 0.8018 (ttm170) cc_final: 0.7783 (mmm-85) REVERT: C 230 MET cc_start: 0.9134 (mmm) cc_final: 0.8725 (mmm) REVERT: C 317 MET cc_start: 0.8280 (tmm) cc_final: 0.8032 (tmm) REVERT: D 140 PHE cc_start: 0.8880 (m-80) cc_final: 0.8383 (m-80) REVERT: E 251 LEU cc_start: 0.9494 (tp) cc_final: 0.9217 (tt) REVERT: E 269 ILE cc_start: 0.9342 (mt) cc_final: 0.9058 (tt) REVERT: E 317 MET cc_start: 0.9005 (tmm) cc_final: 0.8434 (tmm) REVERT: F 62 GLN cc_start: 0.9044 (pt0) cc_final: 0.8360 (pm20) REVERT: F 109 ASP cc_start: 0.8824 (m-30) cc_final: 0.8428 (p0) outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 0.1128 time to fit residues: 11.8995 Evaluate side-chains 44 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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: 8.9990 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 130 HIS A 283 GLN C 32 HIS C 130 HIS C 226 GLN E 261 ASN F 53 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.033914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.025918 restraints weight = 99118.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.026810 restraints weight = 58025.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.027454 restraints weight = 40411.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.027913 restraints weight = 30884.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.028244 restraints weight = 25237.832| |-----------------------------------------------------------------------------| r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12901 Z= 0.232 Angle : 0.687 9.527 17582 Z= 0.347 Chirality : 0.045 0.244 1985 Planarity : 0.003 0.031 2239 Dihedral : 8.295 57.488 2328 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.64 % Favored : 90.23 % Rotamer: Outliers : 0.08 % Allowed : 1.32 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.53 (0.20), residues: 1566 helix: 2.43 (0.26), residues: 393 sheet: -1.40 (0.33), residues: 213 loop : -2.62 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 149 TYR 0.018 0.002 TYR F 190 PHE 0.017 0.002 PHE C 115 TRP 0.036 0.002 TRP E 255 HIS 0.007 0.002 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00499 (12852) covalent geometry : angle 0.67213 (17453) SS BOND : bond 0.00550 ( 18) SS BOND : angle 1.56577 ( 36) hydrogen bonds : bond 0.05843 ( 444) hydrogen bonds : angle 4.71969 ( 1239) link_BETA1-4 : bond 0.00331 ( 13) link_BETA1-4 : angle 1.61578 ( 39) link_BETA1-6 : bond 0.00563 ( 3) link_BETA1-6 : angle 1.14849 ( 9) link_NAG-ASN : bond 0.00404 ( 15) link_NAG-ASN : angle 2.16016 ( 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: 1 poor density : 57 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8881 (mtp) cc_final: 0.8336 (mtm) REVERT: A 317 MET cc_start: 0.8960 (tmm) cc_final: 0.8462 (tmm) REVERT: C 211 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7797 (mmm-85) REVERT: C 230 MET cc_start: 0.9110 (mmm) cc_final: 0.8820 (mmm) REVERT: C 317 MET cc_start: 0.8535 (tmm) cc_final: 0.8216 (tmm) REVERT: D 140 PHE cc_start: 0.9072 (m-80) cc_final: 0.8497 (m-80) REVERT: E 269 ILE cc_start: 0.9343 (mt) cc_final: 0.9077 (tt) REVERT: E 317 MET cc_start: 0.9077 (tmm) cc_final: 0.8413 (tmm) REVERT: F 62 GLN cc_start: 0.9046 (pt0) cc_final: 0.8349 (pm20) REVERT: F 109 ASP cc_start: 0.8916 (m-30) cc_final: 0.8129 (m-30) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.1267 time to fit residues: 10.9251 Evaluate side-chains 40 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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: 7.9990 chunk 139 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.034366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.026350 restraints weight = 96753.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.027267 restraints weight = 56157.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.027928 restraints weight = 38684.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.028402 restraints weight = 29345.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028740 restraints weight = 23855.419| |-----------------------------------------------------------------------------| r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2700 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= 0.148 Angle : 0.603 9.509 17582 Z= 0.305 Chirality : 0.044 0.236 1985 Planarity : 0.003 0.030 2239 Dihedral : 7.841 59.397 2328 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.79 % Favored : 92.08 % 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 : 0.07 % 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 aren not related in a simple way. whole: -1.36 (0.20), residues: 1566 helix: 2.65 (0.26), residues: 394 sheet: -1.42 (0.32), residues: 219 loop : -2.52 (0.17), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 106 TYR 0.017 0.001 TYR F 190 PHE 0.015 0.002 PHE E 115 TRP 0.023 0.001 TRP E 255 HIS 0.006 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00315 (12852) covalent geometry : angle 0.59114 (17453) SS BOND : bond 0.00635 ( 18) SS BOND : angle 1.18431 ( 36) hydrogen bonds : bond 0.05570 ( 444) hydrogen bonds : angle 4.46231 ( 1239) link_BETA1-4 : bond 0.00439 ( 13) link_BETA1-4 : angle 1.38461 ( 39) link_BETA1-6 : bond 0.00526 ( 3) link_BETA1-6 : angle 1.11226 ( 9) link_NAG-ASN : bond 0.00244 ( 15) link_NAG-ASN : angle 1.92648 ( 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 57 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8894 (mtp) cc_final: 0.8368 (mtm) REVERT: A 317 MET cc_start: 0.8990 (tmm) cc_final: 0.8488 (tmm) REVERT: B 27 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8971 (tm-30) REVERT: B 109 ASP cc_start: 0.8950 (m-30) cc_final: 0.8652 (p0) REVERT: C 164 LEU cc_start: 0.9259 (tp) cc_final: 0.8877 (mt) REVERT: C 211 ARG cc_start: 0.8063 (ttm170) cc_final: 0.7858 (mmm-85) REVERT: C 230 MET cc_start: 0.9114 (mmm) cc_final: 0.8804 (mmm) REVERT: C 317 MET cc_start: 0.8543 (tmm) cc_final: 0.8173 (tmm) REVERT: D 118 LEU cc_start: 0.9642 (tp) cc_final: 0.9417 (tt) REVERT: D 140 PHE cc_start: 0.9101 (m-80) cc_final: 0.8588 (m-80) REVERT: E 269 ILE cc_start: 0.9354 (mt) cc_final: 0.9108 (tt) REVERT: E 317 MET cc_start: 0.9043 (tmm) cc_final: 0.8423 (tmm) REVERT: F 17 MET cc_start: 0.8908 (tpt) cc_final: 0.8701 (tpt) REVERT: F 62 GLN cc_start: 0.8994 (pt0) cc_final: 0.8337 (pm20) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1148 time to fit residues: 10.1409 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 : 0.506 ------------------------------------------------------------------------------- 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: 4.9990 chunk 146 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.033382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.025358 restraints weight = 98046.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.026255 restraints weight = 56574.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.026907 restraints weight = 39037.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.027378 restraints weight = 29629.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.027625 restraints weight = 24138.795| |-----------------------------------------------------------------------------| r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12901 Z= 0.263 Angle : 0.716 9.531 17582 Z= 0.359 Chirality : 0.045 0.238 1985 Planarity : 0.003 0.036 2239 Dihedral : 7.826 55.464 2328 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.54 % Favored : 89.34 % Rotamer: Outliers : 0.08 % Allowed : 1.63 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.42 (0.21), residues: 1566 helix: 2.42 (0.26), residues: 405 sheet: -1.36 (0.33), residues: 213 loop : -2.56 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 212 TYR 0.016 0.002 TYR C 195 PHE 0.015 0.002 PHE A 245 TRP 0.024 0.002 TRP E 255 HIS 0.008 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00561 (12852) covalent geometry : angle 0.70254 (17453) SS BOND : bond 0.00466 ( 18) SS BOND : angle 1.57612 ( 36) hydrogen bonds : bond 0.05891 ( 444) hydrogen bonds : angle 4.70960 ( 1239) link_BETA1-4 : bond 0.00377 ( 13) link_BETA1-4 : angle 1.51411 ( 39) link_BETA1-6 : bond 0.00595 ( 3) link_BETA1-6 : angle 1.14580 ( 9) link_NAG-ASN : bond 0.00519 ( 15) link_NAG-ASN : angle 2.21494 ( 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 57 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8643 (m-80) cc_final: 0.8307 (m-80) REVERT: A 230 MET cc_start: 0.8922 (mtp) cc_final: 0.8382 (mtm) REVERT: A 317 MET cc_start: 0.9058 (tmm) cc_final: 0.8519 (tmm) REVERT: B 109 ASP cc_start: 0.8948 (m-30) cc_final: 0.8687 (p0) REVERT: C 164 LEU cc_start: 0.9306 (tp) cc_final: 0.8901 (mt) REVERT: C 230 MET cc_start: 0.9072 (mmm) cc_final: 0.8792 (mmm) REVERT: C 317 MET cc_start: 0.8748 (tmm) cc_final: 0.8284 (tmm) REVERT: D 140 PHE cc_start: 0.9215 (m-80) cc_final: 0.8746 (m-80) REVERT: E 269 ILE cc_start: 0.9394 (mt) cc_final: 0.9157 (tt) REVERT: E 317 MET cc_start: 0.9107 (tmm) cc_final: 0.8416 (tmm) REVERT: F 17 MET cc_start: 0.9010 (tpt) cc_final: 0.8800 (tpt) REVERT: F 62 GLN cc_start: 0.9024 (pt0) cc_final: 0.8199 (pm20) outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 0.1269 time to fit residues: 10.8378 Evaluate side-chains 40 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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: 0.9980 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 108 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 111 HIS F 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.034581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.026574 restraints weight = 94554.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.027533 restraints weight = 54329.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.028184 restraints weight = 36953.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.028674 restraints weight = 27994.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.029031 restraints weight = 22727.484| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12901 Z= 0.120 Angle : 0.599 9.517 17582 Z= 0.301 Chirality : 0.044 0.237 1985 Planarity : 0.003 0.030 2239 Dihedral : 7.506 58.018 2328 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.13 (0.21), residues: 1566 helix: 2.80 (0.26), residues: 397 sheet: -1.31 (0.34), residues: 204 loop : -2.35 (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 F 190 PHE 0.018 0.001 PHE E 115 TRP 0.026 0.002 TRP C 255 HIS 0.005 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00249 (12852) covalent geometry : angle 0.58718 (17453) SS BOND : bond 0.00431 ( 18) SS BOND : angle 1.34127 ( 36) hydrogen bonds : bond 0.05511 ( 444) hydrogen bonds : angle 4.35352 ( 1239) link_BETA1-4 : bond 0.00483 ( 13) link_BETA1-4 : angle 1.32426 ( 39) link_BETA1-6 : bond 0.00521 ( 3) link_BETA1-6 : angle 1.10195 ( 9) link_NAG-ASN : bond 0.00207 ( 15) link_NAG-ASN : angle 1.82582 ( 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 60 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8639 (m-80) cc_final: 0.8239 (m-80) REVERT: A 230 MET cc_start: 0.8844 (mtp) cc_final: 0.8327 (mtm) REVERT: A 317 MET cc_start: 0.9043 (tmm) cc_final: 0.8507 (tmm) REVERT: B 27 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8983 (tm-30) REVERT: B 109 ASP cc_start: 0.8880 (m-30) cc_final: 0.8623 (p0) REVERT: B 149 MET cc_start: 0.8958 (mmt) cc_final: 0.8703 (mmt) REVERT: C 164 LEU cc_start: 0.9277 (tp) cc_final: 0.8862 (mt) REVERT: C 211 ARG cc_start: 0.8987 (ttm110) cc_final: 0.8254 (mmm-85) REVERT: C 230 MET cc_start: 0.9117 (mmm) cc_final: 0.8847 (mmm) REVERT: C 317 MET cc_start: 0.8708 (tmm) cc_final: 0.8289 (tmm) REVERT: D 140 PHE cc_start: 0.9223 (m-80) cc_final: 0.8768 (m-80) REVERT: E 269 ILE cc_start: 0.9352 (mt) cc_final: 0.9123 (tt) REVERT: E 317 MET cc_start: 0.9044 (tmm) cc_final: 0.8415 (tmm) REVERT: F 17 MET cc_start: 0.8971 (tpt) cc_final: 0.8731 (tpt) REVERT: F 62 GLN cc_start: 0.8953 (pt0) cc_final: 0.8185 (pm20) REVERT: F 109 ASP cc_start: 0.8707 (m-30) cc_final: 0.8505 (m-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1256 time to fit residues: 11.3570 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 : 0.542 ------------------------------------------------------------------------------- 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: 5.9990 chunk 50 optimal weight: 0.3980 chunk 133 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.034084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.026108 restraints weight = 95730.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.027007 restraints weight = 55482.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.027661 restraints weight = 38349.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.028130 restraints weight = 28999.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.028469 restraints weight = 23666.209| |-----------------------------------------------------------------------------| r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12901 Z= 0.185 Angle : 0.637 9.565 17582 Z= 0.319 Chirality : 0.044 0.239 1985 Planarity : 0.003 0.030 2239 Dihedral : 7.493 55.817 2328 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.07 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.07 (0.21), residues: 1566 helix: 2.79 (0.26), residues: 402 sheet: -1.32 (0.34), residues: 204 loop : -2.30 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 211 TYR 0.015 0.001 TYR C 195 PHE 0.014 0.002 PHE A 213 TRP 0.023 0.002 TRP C 255 HIS 0.006 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00399 (12852) covalent geometry : angle 0.62466 (17453) SS BOND : bond 0.00423 ( 18) SS BOND : angle 1.26763 ( 36) hydrogen bonds : bond 0.05507 ( 444) hydrogen bonds : angle 4.46696 ( 1239) link_BETA1-4 : bond 0.00378 ( 13) link_BETA1-4 : angle 1.38712 ( 39) link_BETA1-6 : bond 0.00563 ( 3) link_BETA1-6 : angle 1.11237 ( 9) link_NAG-ASN : bond 0.00332 ( 15) link_NAG-ASN : angle 1.94903 ( 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 61 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8648 (m-80) cc_final: 0.8302 (m-80) REVERT: A 230 MET cc_start: 0.8894 (mtp) cc_final: 0.8352 (mtm) REVERT: A 317 MET cc_start: 0.9054 (tmm) cc_final: 0.8542 (tmm) REVERT: B 27 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8983 (tm-30) REVERT: B 149 MET cc_start: 0.8977 (mmt) cc_final: 0.8713 (mmt) REVERT: C 164 LEU cc_start: 0.9316 (tp) cc_final: 0.8879 (mt) REVERT: C 211 ARG cc_start: 0.8967 (ttm110) cc_final: 0.8173 (mmm-85) REVERT: C 230 MET cc_start: 0.9035 (mmm) cc_final: 0.8789 (mmm) REVERT: C 317 MET cc_start: 0.8760 (tmm) cc_final: 0.8329 (tmm) REVERT: D 140 PHE cc_start: 0.9285 (m-80) cc_final: 0.8843 (m-80) REVERT: E 269 ILE cc_start: 0.9413 (mt) cc_final: 0.9189 (tt) REVERT: E 317 MET cc_start: 0.9082 (tmm) cc_final: 0.8369 (tmm) REVERT: F 62 GLN cc_start: 0.8989 (pt0) cc_final: 0.8201 (pm20) REVERT: F 109 ASP cc_start: 0.8726 (m-30) cc_final: 0.8454 (m-30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1152 time to fit residues: 10.9536 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 : 0.489 ------------------------------------------------------------------------------- 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: 2.9990 chunk 125 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2748 r_free = 0.2748 target = 0.033817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.025757 restraints weight = 97347.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.026660 restraints weight = 56185.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.027314 restraints weight = 38789.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.027771 restraints weight = 29449.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.028129 restraints weight = 24075.804| |-----------------------------------------------------------------------------| r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12901 Z= 0.198 Angle : 0.651 9.541 17582 Z= 0.328 Chirality : 0.044 0.234 1985 Planarity : 0.003 0.030 2239 Dihedral : 7.525 55.945 2328 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.68 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.10 (0.21), residues: 1566 helix: 2.72 (0.26), residues: 405 sheet: -1.34 (0.34), residues: 204 loop : -2.32 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 211 TYR 0.016 0.002 TYR C 195 PHE 0.024 0.002 PHE B 140 TRP 0.023 0.002 TRP C 255 HIS 0.007 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00424 (12852) covalent geometry : angle 0.63794 (17453) SS BOND : bond 0.00483 ( 18) SS BOND : angle 1.63906 ( 36) hydrogen bonds : bond 0.05611 ( 444) hydrogen bonds : angle 4.58740 ( 1239) link_BETA1-4 : bond 0.00370 ( 13) link_BETA1-4 : angle 1.37378 ( 39) link_BETA1-6 : bond 0.00576 ( 3) link_BETA1-6 : angle 1.12304 ( 9) link_NAG-ASN : bond 0.00360 ( 15) link_NAG-ASN : angle 1.95434 ( 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 58 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8631 (m-80) cc_final: 0.8319 (m-80) REVERT: A 211 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.8097 (ttm-80) REVERT: A 230 MET cc_start: 0.8837 (mtp) cc_final: 0.8307 (mtm) REVERT: A 317 MET cc_start: 0.9055 (tmm) cc_final: 0.8557 (tmm) REVERT: B 27 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8945 (tm-30) REVERT: C 164 LEU cc_start: 0.9350 (tp) cc_final: 0.8902 (mt) REVERT: C 211 ARG cc_start: 0.8884 (ttm110) cc_final: 0.8056 (mmm-85) REVERT: C 230 MET cc_start: 0.9016 (mmm) cc_final: 0.8760 (mmm) REVERT: C 317 MET cc_start: 0.8814 (tmm) cc_final: 0.8434 (tmm) REVERT: D 140 PHE cc_start: 0.9267 (m-80) cc_final: 0.8886 (m-80) REVERT: E 269 ILE cc_start: 0.9369 (mt) cc_final: 0.9161 (tt) REVERT: E 317 MET cc_start: 0.9065 (tmm) cc_final: 0.8357 (tmm) REVERT: F 62 GLN cc_start: 0.9003 (pt0) cc_final: 0.8236 (pm20) REVERT: F 109 ASP cc_start: 0.8711 (m-30) cc_final: 0.8492 (m-30) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1220 time to fit residues: 10.6672 Evaluate side-chains 43 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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: 4.9990 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2767 r_free = 0.2767 target = 0.034294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.026235 restraints weight = 96682.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.027148 restraints weight = 55660.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.027810 restraints weight = 38378.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.028299 restraints weight = 29023.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.028622 restraints weight = 23671.738| |-----------------------------------------------------------------------------| r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12901 Z= 0.146 Angle : 0.618 9.558 17582 Z= 0.310 Chirality : 0.044 0.235 1985 Planarity : 0.003 0.029 2239 Dihedral : 7.406 58.975 2328 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.37 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.98 (0.21), residues: 1566 helix: 2.86 (0.26), residues: 402 sheet: -1.26 (0.34), residues: 204 loop : -2.25 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 127 TYR 0.018 0.001 TYR C 256 PHE 0.015 0.002 PHE E 115 TRP 0.018 0.002 TRP E 255 HIS 0.005 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00312 (12852) covalent geometry : angle 0.60540 (17453) SS BOND : bond 0.00352 ( 18) SS BOND : angle 1.60730 ( 36) hydrogen bonds : bond 0.05450 ( 444) hydrogen bonds : angle 4.45270 ( 1239) link_BETA1-4 : bond 0.00418 ( 13) link_BETA1-4 : angle 1.34095 ( 39) link_BETA1-6 : bond 0.00522 ( 3) link_BETA1-6 : angle 1.08744 ( 9) link_NAG-ASN : bond 0.00252 ( 15) link_NAG-ASN : angle 1.78501 ( 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 57 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8648 (m-80) cc_final: 0.8288 (m-80) REVERT: A 211 ARG cc_start: 0.8369 (ttm-80) cc_final: 0.8131 (ttm-80) REVERT: A 230 MET cc_start: 0.8799 (mtp) cc_final: 0.8272 (mtm) REVERT: A 317 MET cc_start: 0.9097 (tmm) cc_final: 0.8550 (tmm) REVERT: B 27 GLN cc_start: 0.9283 (tm-30) cc_final: 0.8982 (tm-30) REVERT: C 164 LEU cc_start: 0.9321 (tp) cc_final: 0.8874 (mt) REVERT: C 211 ARG cc_start: 0.8891 (ttm110) cc_final: 0.8135 (mmm-85) REVERT: C 230 MET cc_start: 0.9097 (mmm) cc_final: 0.8839 (mmm) REVERT: C 317 MET cc_start: 0.8794 (tmm) cc_final: 0.8353 (tmm) REVERT: D 140 PHE cc_start: 0.9239 (m-80) cc_final: 0.8917 (m-80) REVERT: E 269 ILE cc_start: 0.9385 (mt) cc_final: 0.9180 (tt) REVERT: E 317 MET cc_start: 0.9059 (tmm) cc_final: 0.8426 (tmm) REVERT: F 62 GLN cc_start: 0.8974 (pt0) cc_final: 0.8232 (pm20) REVERT: F 109 ASP cc_start: 0.8697 (m-30) cc_final: 0.8430 (m-30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1326 time to fit residues: 11.1940 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 : 0.614 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.035060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.027002 restraints weight = 95877.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.027969 restraints weight = 54960.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.028660 restraints weight = 37331.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.029143 restraints weight = 28080.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.029443 restraints weight = 22876.975| |-----------------------------------------------------------------------------| r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3479 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= 0.108 Angle : 0.587 9.538 17582 Z= 0.294 Chirality : 0.043 0.230 1985 Planarity : 0.003 0.030 2239 Dihedral : 7.112 55.789 2328 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.82 (0.21), residues: 1566 helix: 3.03 (0.25), residues: 402 sheet: -1.07 (0.35), residues: 204 loop : -2.19 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 127 TYR 0.023 0.001 TYR F 22 PHE 0.015 0.001 PHE E 115 TRP 0.016 0.001 TRP C 255 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00223 (12852) covalent geometry : angle 0.57712 (17453) SS BOND : bond 0.00324 ( 18) SS BOND : angle 1.35234 ( 36) hydrogen bonds : bond 0.05046 ( 444) hydrogen bonds : angle 4.30133 ( 1239) link_BETA1-4 : bond 0.00501 ( 13) link_BETA1-4 : angle 1.27959 ( 39) link_BETA1-6 : bond 0.00522 ( 3) link_BETA1-6 : angle 1.09077 ( 9) link_NAG-ASN : bond 0.00167 ( 15) link_NAG-ASN : angle 1.59873 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.03 seconds wall clock time: 31 minutes 2.82 seconds (1862.82 seconds total)