Starting phenix.real_space_refine on Wed Jul 30 22:33:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hjr_0237/07_2025/6hjr_0237.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hjr_0237/07_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_0237/07_2025/6hjr_0237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hjr_0237/07_2025/6hjr_0237.map" model { file = "/net/cci-nas-00/data/ceres_data/6hjr_0237/07_2025/6hjr_0237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hjr_0237/07_2025/6hjr_0237.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 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: {'TYR:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 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: {'TYR:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 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: 9.23, per 1000 atoms: 0.73 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: 3.29 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.31 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: 3.33 Time building geometry restraints manager: 3.88 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 326 or resid 401)) selection = chain 'C' selection = (chain 'E' and (resid 5 through 326 or resid 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: 6.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.610 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.520 ------------------------------------------------------------------------------- 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 : 6.58 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.046 0.005 TRP A 255 HIS 0.022 0.004 HIS C 276 PHE 0.037 0.004 PHE D 140 TYR 0.044 0.003 TYR C 195 ARG 0.009 0.001 ARG C 106 Details of bonding type rmsd link_NAG-ASN : bond 0.01111 ( 15) link_NAG-ASN : angle 4.40235 ( 45) link_BETA1-4 : bond 0.00715 ( 13) link_BETA1-4 : angle 2.34016 ( 39) hydrogen bonds : bond 0.18649 ( 444) hydrogen bonds : angle 6.74992 ( 1239) link_BETA1-6 : bond 0.00584 ( 3) link_BETA1-6 : angle 2.17037 ( 9) SS BOND : bond 0.00788 ( 18) SS BOND : angle 1.68776 ( 36) covalent geometry : bond 0.00943 (12852) covalent geometry : angle 1.12941 (17453) *********************** 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 : 1.378 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: 0.8224 (m-80) REVERT: B 62 GLN cc_start: 0.9129 (pt0) cc_final: 0.8716 (pm20) REVERT: C 251 LEU cc_start: 0.9512 (tp) cc_final: 0.9116 (tt) REVERT: D 94 TYR cc_start: 0.9635 (t80) cc_final: 0.9350 (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) REVERT: F 150 GLU cc_start: 0.9354 (tp30) cc_final: 0.8857 (tp30) outliers start: 9 outliers final: 0 residues processed: 105 average time/residue: 0.2764 time to fit residues: 41.2228 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 : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN A 286 HIS C 130 HIS C 226 GLN C 286 HIS E 32 HIS E 108 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.034664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.026572 restraints weight = 94244.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.027471 restraints weight = 54705.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.028132 restraints weight = 37869.846| |-----------------------------------------------------------------------------| r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12901 Z= 0.152 Angle : 0.707 9.914 17582 Z= 0.356 Chirality : 0.046 0.263 1985 Planarity : 0.004 0.039 2239 Dihedral : 10.640 67.760 2328 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.92 % Favored : 91.95 % Rotamer: Outliers : 0.15 % Allowed : 1.08 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.19), residues: 1566 helix: 1.62 (0.25), residues: 397 sheet: -1.89 (0.32), residues: 204 loop : -2.92 (0.16), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 92 HIS 0.006 0.001 HIS C 276 PHE 0.038 0.002 PHE B 140 TYR 0.020 0.002 TYR F 190 ARG 0.006 0.001 ARG D 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 15) link_NAG-ASN : angle 2.48753 ( 45) link_BETA1-4 : bond 0.00544 ( 13) link_BETA1-4 : angle 1.81593 ( 39) hydrogen bonds : bond 0.06745 ( 444) hydrogen bonds : angle 5.09750 ( 1239) link_BETA1-6 : bond 0.00406 ( 3) link_BETA1-6 : angle 1.37859 ( 9) SS BOND : bond 0.00654 ( 18) SS BOND : angle 1.46949 ( 36) covalent geometry : bond 0.00312 (12852) covalent geometry : angle 0.68945 (17453) *********************** 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 76 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8650 (tmm) cc_final: 0.8376 (tmm) REVERT: B 62 GLN cc_start: 0.9043 (pt0) cc_final: 0.8517 (pm20) REVERT: B 109 ASP cc_start: 0.9188 (p0) cc_final: 0.8825 (m-30) REVERT: C 7 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9300 (mp) REVERT: C 230 MET cc_start: 0.8590 (mtp) cc_final: 0.8380 (mtp) REVERT: C 251 LEU cc_start: 0.9461 (tp) cc_final: 0.9081 (tt) REVERT: C 317 MET cc_start: 0.8252 (tmm) cc_final: 0.8021 (tmm) REVERT: D 120 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8457 (mp0) REVERT: D 133 ILE cc_start: 0.9676 (pt) cc_final: 0.9101 (mm) REVERT: E 239 GLN cc_start: 0.9714 (pm20) cc_final: 0.8925 (pm20) REVERT: E 317 MET cc_start: 0.9003 (tmm) cc_final: 0.8454 (tmm) REVERT: F 62 GLN cc_start: 0.9107 (pt0) cc_final: 0.8400 (pm20) outliers start: 2 outliers final: 0 residues processed: 76 average time/residue: 0.2665 time to fit residues: 29.9997 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 : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 ASN F 53 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.032615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2369 r_free = 0.2369 target = 0.024769 restraints weight = 101824.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.025631 restraints weight = 60551.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.026233 restraints weight = 42120.156| |-----------------------------------------------------------------------------| r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 12901 Z= 0.376 Angle : 0.856 9.622 17582 Z= 0.431 Chirality : 0.048 0.263 1985 Planarity : 0.004 0.031 2239 Dihedral : 9.390 56.826 2328 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.37 % Favored : 88.51 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.20), residues: 1566 helix: 1.64 (0.25), residues: 402 sheet: -1.94 (0.32), residues: 207 loop : -2.85 (0.17), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 127 HIS 0.011 0.003 HIS A 183 PHE 0.028 0.003 PHE B 140 TYR 0.021 0.003 TYR E 209 ARG 0.005 0.001 ARG A 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00695 ( 15) link_NAG-ASN : angle 2.66581 ( 45) link_BETA1-4 : bond 0.00489 ( 13) link_BETA1-4 : angle 1.87192 ( 39) hydrogen bonds : bond 0.06822 ( 444) hydrogen bonds : angle 5.26528 ( 1239) link_BETA1-6 : bond 0.00598 ( 3) link_BETA1-6 : angle 1.21445 ( 9) SS BOND : bond 0.00620 ( 18) SS BOND : angle 1.45615 ( 36) covalent geometry : bond 0.00804 (12852) covalent geometry : angle 0.84118 (17453) *********************** 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 56 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8935 (tmm) cc_final: 0.8455 (tmm) REVERT: B 62 GLN cc_start: 0.9136 (pt0) cc_final: 0.8500 (pp30) REVERT: B 109 ASP cc_start: 0.9270 (p0) cc_final: 0.9036 (m-30) REVERT: B 140 PHE cc_start: 0.9156 (m-80) cc_final: 0.8887 (m-80) REVERT: C 230 MET cc_start: 0.8876 (mtp) cc_final: 0.8471 (mtp) REVERT: C 251 LEU cc_start: 0.9489 (tp) cc_final: 0.9057 (tt) REVERT: C 317 MET cc_start: 0.8613 (tmm) cc_final: 0.8295 (tmm) REVERT: D 120 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8729 (mt-10) REVERT: D 140 PHE cc_start: 0.9219 (m-80) cc_final: 0.8497 (m-80) REVERT: D 149 MET cc_start: 0.9346 (mmp) cc_final: 0.9082 (mmm) REVERT: E 269 ILE cc_start: 0.9367 (mt) cc_final: 0.9119 (tt) REVERT: E 317 MET cc_start: 0.9151 (tmm) cc_final: 0.8486 (tmm) REVERT: F 62 GLN cc_start: 0.9179 (pt0) cc_final: 0.8468 (pm20) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2228 time to fit residues: 19.9454 Evaluate side-chains 37 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.033253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.025258 restraints weight = 96354.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.026158 restraints weight = 55648.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.026797 restraints weight = 38259.279| |-----------------------------------------------------------------------------| r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12901 Z= 0.223 Angle : 0.690 9.537 17582 Z= 0.351 Chirality : 0.045 0.245 1985 Planarity : 0.003 0.032 2239 Dihedral : 8.623 56.679 2328 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.00 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.20), residues: 1566 helix: 2.08 (0.25), residues: 399 sheet: -1.87 (0.32), residues: 213 loop : -2.69 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 255 HIS 0.006 0.002 HIS E 276 PHE 0.022 0.002 PHE D 140 TYR 0.020 0.002 TYR E 161 ARG 0.004 0.000 ARG B 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 15) link_NAG-ASN : angle 2.25264 ( 45) link_BETA1-4 : bond 0.00391 ( 13) link_BETA1-4 : angle 1.57523 ( 39) hydrogen bonds : bond 0.06283 ( 444) hydrogen bonds : angle 4.83146 ( 1239) link_BETA1-6 : bond 0.00603 ( 3) link_BETA1-6 : angle 1.15357 ( 9) SS BOND : bond 0.00497 ( 18) SS BOND : angle 1.29651 ( 36) covalent geometry : bond 0.00479 (12852) covalent geometry : angle 0.67556 (17453) *********************** 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 53 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8708 (m-80) cc_final: 0.8229 (m-80) REVERT: A 230 MET cc_start: 0.8650 (mtp) cc_final: 0.8358 (mtp) REVERT: A 317 MET cc_start: 0.9015 (tmm) cc_final: 0.8540 (tmm) REVERT: B 62 GLN cc_start: 0.9104 (pt0) cc_final: 0.8513 (pp30) REVERT: B 140 PHE cc_start: 0.9090 (m-80) cc_final: 0.8854 (m-80) REVERT: C 230 MET cc_start: 0.8923 (mtp) cc_final: 0.8518 (mtp) REVERT: C 317 MET cc_start: 0.8696 (tmm) cc_final: 0.8281 (tmm) REVERT: D 120 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8704 (mt-10) REVERT: D 140 PHE cc_start: 0.9142 (m-80) cc_final: 0.8502 (m-80) REVERT: E 269 ILE cc_start: 0.9339 (mt) cc_final: 0.9104 (tt) REVERT: E 317 MET cc_start: 0.9043 (tmm) cc_final: 0.8365 (tmm) REVERT: F 62 GLN cc_start: 0.9123 (pt0) cc_final: 0.8343 (pm20) REVERT: F 109 ASP cc_start: 0.9030 (m-30) cc_final: 0.8153 (m-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2557 time to fit residues: 21.0997 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 : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 48 optimal weight: 0.3980 chunk 102 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 overall best weight: 5.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.032172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.024379 restraints weight = 99743.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.025228 restraints weight = 58118.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.025834 restraints weight = 40360.273| |-----------------------------------------------------------------------------| r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 12901 Z= 0.347 Angle : 0.804 9.608 17582 Z= 0.405 Chirality : 0.046 0.241 1985 Planarity : 0.004 0.032 2239 Dihedral : 8.574 56.564 2328 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.39 % Favored : 87.48 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.20), residues: 1566 helix: 1.76 (0.25), residues: 404 sheet: -1.88 (0.32), residues: 213 loop : -2.79 (0.17), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 255 HIS 0.009 0.002 HIS A 183 PHE 0.027 0.003 PHE B 140 TYR 0.023 0.002 TYR F 24 ARG 0.005 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00710 ( 15) link_NAG-ASN : angle 2.45961 ( 45) link_BETA1-4 : bond 0.00449 ( 13) link_BETA1-4 : angle 1.60443 ( 39) hydrogen bonds : bond 0.06459 ( 444) hydrogen bonds : angle 5.07409 ( 1239) link_BETA1-6 : bond 0.00516 ( 3) link_BETA1-6 : angle 1.16101 ( 9) SS BOND : bond 0.00570 ( 18) SS BOND : angle 1.33809 ( 36) covalent geometry : bond 0.00741 (12852) covalent geometry : angle 0.79113 (17453) *********************** 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 49 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8837 (m-80) cc_final: 0.8512 (m-80) REVERT: A 230 MET cc_start: 0.8685 (mtp) cc_final: 0.8331 (mtp) REVERT: A 317 MET cc_start: 0.9109 (tmm) cc_final: 0.8568 (tmm) REVERT: B 62 GLN cc_start: 0.9228 (pt0) cc_final: 0.8726 (pp30) REVERT: C 230 MET cc_start: 0.8955 (mtp) cc_final: 0.8515 (mtp) REVERT: C 317 MET cc_start: 0.8935 (tmm) cc_final: 0.8503 (tmm) REVERT: D 120 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8826 (mt-10) REVERT: D 140 PHE cc_start: 0.9282 (m-80) cc_final: 0.8717 (m-80) REVERT: E 269 ILE cc_start: 0.9380 (mt) cc_final: 0.9165 (tt) REVERT: E 317 MET cc_start: 0.9154 (tmm) cc_final: 0.8393 (tmm) REVERT: F 62 GLN cc_start: 0.9149 (pt0) cc_final: 0.8405 (pm20) REVERT: F 109 ASP cc_start: 0.8935 (m-30) cc_final: 0.8652 (m-30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2355 time to fit residues: 18.6396 Evaluate side-chains 37 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 192 GLN B 111 HIS ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.033906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.025828 restraints weight = 97269.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.026741 restraints weight = 55386.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.027398 restraints weight = 37878.775| |-----------------------------------------------------------------------------| r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12901 Z= 0.138 Angle : 0.636 9.902 17582 Z= 0.320 Chirality : 0.045 0.244 1985 Planarity : 0.003 0.034 2239 Dihedral : 8.010 59.677 2328 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.28 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.21), residues: 1566 helix: 2.57 (0.26), residues: 394 sheet: -1.65 (0.33), residues: 198 loop : -2.48 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 255 HIS 0.003 0.001 HIS E 183 PHE 0.018 0.002 PHE E 115 TYR 0.018 0.001 TYR E 161 ARG 0.006 0.000 ARG C 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 15) link_NAG-ASN : angle 1.95785 ( 45) link_BETA1-4 : bond 0.00444 ( 13) link_BETA1-4 : angle 1.41354 ( 39) hydrogen bonds : bond 0.05915 ( 444) hydrogen bonds : angle 4.52360 ( 1239) link_BETA1-6 : bond 0.00504 ( 3) link_BETA1-6 : angle 1.08793 ( 9) SS BOND : bond 0.00313 ( 18) SS BOND : angle 1.25046 ( 36) covalent geometry : bond 0.00294 (12852) covalent geometry : angle 0.62441 (17453) *********************** 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 56 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8661 (m-80) cc_final: 0.8427 (m-80) REVERT: A 230 MET cc_start: 0.8666 (mtp) cc_final: 0.8377 (mtp) REVERT: A 317 MET cc_start: 0.9085 (tmm) cc_final: 0.8528 (tmm) REVERT: B 27 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8939 (tm-30) REVERT: B 62 GLN cc_start: 0.9160 (pt0) cc_final: 0.8634 (pm20) REVERT: B 109 ASP cc_start: 0.8884 (m-30) cc_final: 0.8670 (p0) REVERT: B 140 PHE cc_start: 0.8925 (m-80) cc_final: 0.8674 (m-80) REVERT: C 230 MET cc_start: 0.8870 (mtp) cc_final: 0.8524 (mtp) REVERT: C 317 MET cc_start: 0.8835 (tmm) cc_final: 0.8339 (tmm) REVERT: D 120 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8745 (mt-10) REVERT: D 140 PHE cc_start: 0.9213 (m-80) cc_final: 0.8717 (m-80) REVERT: E 115 PHE cc_start: 0.8490 (m-80) cc_final: 0.8260 (m-10) REVERT: E 269 ILE cc_start: 0.9329 (mt) cc_final: 0.9128 (tt) REVERT: E 317 MET cc_start: 0.9097 (tmm) cc_final: 0.8378 (tmm) REVERT: F 62 GLN cc_start: 0.9090 (pt0) cc_final: 0.8251 (pm20) REVERT: F 109 ASP cc_start: 0.8823 (m-30) cc_final: 0.8543 (m-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2259 time to fit residues: 20.3824 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 : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 100 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.026761 restraints weight = 94027.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.027700 restraints weight = 53262.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.028381 restraints weight = 36152.084| |-----------------------------------------------------------------------------| r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12901 Z= 0.110 Angle : 0.595 9.603 17582 Z= 0.299 Chirality : 0.044 0.235 1985 Planarity : 0.003 0.036 2239 Dihedral : 7.507 59.155 2328 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.85 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.21), residues: 1566 helix: 2.73 (0.25), residues: 397 sheet: -1.46 (0.35), residues: 184 loop : -2.38 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 255 HIS 0.004 0.001 HIS F 26 PHE 0.029 0.002 PHE C 115 TYR 0.017 0.001 TYR F 190 ARG 0.005 0.000 ARG F 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 15) link_NAG-ASN : angle 1.76400 ( 45) link_BETA1-4 : bond 0.00518 ( 13) link_BETA1-4 : angle 1.35970 ( 39) hydrogen bonds : bond 0.05400 ( 444) hydrogen bonds : angle 4.30851 ( 1239) link_BETA1-6 : bond 0.00574 ( 3) link_BETA1-6 : angle 1.11431 ( 9) SS BOND : bond 0.00296 ( 18) SS BOND : angle 0.98238 ( 36) covalent geometry : bond 0.00227 (12852) covalent geometry : angle 0.58507 (17453) *********************** 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 65 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8566 (m-80) cc_final: 0.8322 (m-80) REVERT: A 230 MET cc_start: 0.8744 (mtp) cc_final: 0.8401 (mtp) REVERT: A 317 MET cc_start: 0.9091 (tmm) cc_final: 0.8489 (tmm) REVERT: B 27 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8942 (tm-30) REVERT: B 62 GLN cc_start: 0.9017 (pt0) cc_final: 0.8732 (pp30) REVERT: B 140 PHE cc_start: 0.8857 (m-80) cc_final: 0.8535 (m-80) REVERT: C 230 MET cc_start: 0.8841 (mtp) cc_final: 0.8511 (mtp) REVERT: C 317 MET cc_start: 0.8779 (tmm) cc_final: 0.8353 (tmm) REVERT: D 120 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8668 (mt-10) REVERT: D 140 PHE cc_start: 0.9171 (m-80) cc_final: 0.8587 (m-80) REVERT: E 317 MET cc_start: 0.9036 (tmm) cc_final: 0.8430 (tmm) REVERT: F 62 GLN cc_start: 0.9032 (pt0) cc_final: 0.8138 (pm20) REVERT: F 109 ASP cc_start: 0.8728 (m-30) cc_final: 0.8502 (m-30) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2382 time to fit residues: 24.9493 Evaluate side-chains 44 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 155 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 30.0000 chunk 74 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN C 150 ASN ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.033165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.025278 restraints weight = 100950.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.026145 restraints weight = 58335.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.026787 restraints weight = 40248.419| |-----------------------------------------------------------------------------| r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12901 Z= 0.279 Angle : 0.714 9.587 17582 Z= 0.361 Chirality : 0.045 0.236 1985 Planarity : 0.003 0.032 2239 Dihedral : 7.787 56.245 2328 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.47 % Favored : 89.40 % Rotamer: Outliers : 0.08 % Allowed : 1.08 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.21), residues: 1566 helix: 2.35 (0.26), residues: 411 sheet: -1.52 (0.33), residues: 219 loop : -2.49 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 255 HIS 0.009 0.002 HIS E 183 PHE 0.015 0.002 PHE A 245 TYR 0.022 0.002 TYR C 161 ARG 0.004 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 15) link_NAG-ASN : angle 2.07947 ( 45) link_BETA1-4 : bond 0.00394 ( 13) link_BETA1-4 : angle 1.47476 ( 39) hydrogen bonds : bond 0.05754 ( 444) hydrogen bonds : angle 4.64081 ( 1239) link_BETA1-6 : bond 0.00576 ( 3) link_BETA1-6 : angle 1.11138 ( 9) SS BOND : bond 0.00429 ( 18) SS BOND : angle 1.16225 ( 36) covalent geometry : bond 0.00595 (12852) covalent geometry : angle 0.70283 (17453) *********************** 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 53 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8786 (m-80) cc_final: 0.8564 (m-80) REVERT: A 230 MET cc_start: 0.8785 (mtp) cc_final: 0.8397 (mtp) REVERT: A 317 MET cc_start: 0.9138 (tmm) cc_final: 0.8524 (tmm) REVERT: B 27 GLN cc_start: 0.9329 (tm-30) cc_final: 0.8937 (tm-30) REVERT: B 62 GLN cc_start: 0.9147 (pt0) cc_final: 0.8764 (pp30) REVERT: B 140 PHE cc_start: 0.8981 (m-80) cc_final: 0.8661 (m-80) REVERT: C 164 LEU cc_start: 0.9407 (tp) cc_final: 0.8959 (mt) REVERT: C 230 MET cc_start: 0.8953 (mtp) cc_final: 0.8535 (mtp) REVERT: C 317 MET cc_start: 0.8900 (tmm) cc_final: 0.8478 (tmm) REVERT: D 59 MET cc_start: 0.8741 (tpt) cc_final: 0.8476 (tpp) REVERT: D 140 PHE cc_start: 0.9357 (m-80) cc_final: 0.8858 (m-80) REVERT: E 115 PHE cc_start: 0.8457 (m-80) cc_final: 0.8212 (m-10) REVERT: E 317 MET cc_start: 0.9139 (tmm) cc_final: 0.8378 (tmm) REVERT: F 62 GLN cc_start: 0.9093 (pt0) cc_final: 0.8293 (pm20) REVERT: F 109 ASP cc_start: 0.8878 (m-30) cc_final: 0.8620 (m-30) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.2037 time to fit residues: 17.9275 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 : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 52 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.034154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.026216 restraints weight = 95815.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.027134 restraints weight = 54724.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.027792 restraints weight = 37348.521| |-----------------------------------------------------------------------------| r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12901 Z= 0.127 Angle : 0.605 9.578 17582 Z= 0.304 Chirality : 0.043 0.231 1985 Planarity : 0.003 0.032 2239 Dihedral : 7.558 58.390 2328 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.17 % Favored : 91.70 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.21), residues: 1566 helix: 2.68 (0.26), residues: 405 sheet: -1.32 (0.34), residues: 204 loop : -2.32 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 255 HIS 0.005 0.001 HIS C 130 PHE 0.019 0.002 PHE C 115 TYR 0.015 0.001 TYR C 161 ARG 0.002 0.000 ARG D 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 15) link_NAG-ASN : angle 1.76462 ( 45) link_BETA1-4 : bond 0.00438 ( 13) link_BETA1-4 : angle 1.36567 ( 39) hydrogen bonds : bond 0.05545 ( 444) hydrogen bonds : angle 4.32994 ( 1239) link_BETA1-6 : bond 0.00569 ( 3) link_BETA1-6 : angle 1.12859 ( 9) SS BOND : bond 0.00433 ( 18) SS BOND : angle 1.30850 ( 36) covalent geometry : bond 0.00268 (12852) covalent geometry : angle 0.59383 (17453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8702 (m-80) cc_final: 0.8494 (m-80) REVERT: A 230 MET cc_start: 0.8716 (mtp) cc_final: 0.8365 (mtp) REVERT: A 317 MET cc_start: 0.9128 (tmm) cc_final: 0.8497 (tmm) REVERT: B 27 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8929 (tm-30) REVERT: B 62 GLN cc_start: 0.9119 (pt0) cc_final: 0.8730 (pp30) REVERT: B 140 PHE cc_start: 0.8924 (m-80) cc_final: 0.8644 (m-80) REVERT: C 164 LEU cc_start: 0.9338 (tp) cc_final: 0.8922 (mt) REVERT: C 230 MET cc_start: 0.8911 (mtp) cc_final: 0.8560 (mtp) REVERT: C 317 MET cc_start: 0.8890 (tmm) cc_final: 0.8369 (tmm) REVERT: D 59 MET cc_start: 0.8715 (tpt) cc_final: 0.8463 (tpp) REVERT: D 140 PHE cc_start: 0.9284 (m-80) cc_final: 0.8870 (m-80) REVERT: E 115 PHE cc_start: 0.8525 (m-80) cc_final: 0.8253 (m-10) REVERT: E 317 MET cc_start: 0.9097 (tmm) cc_final: 0.8383 (tmm) REVERT: F 62 GLN cc_start: 0.9045 (pt0) cc_final: 0.8193 (pm20) REVERT: F 109 ASP cc_start: 0.8833 (m-30) cc_final: 0.8546 (m-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2662 time to fit residues: 24.4057 Evaluate side-chains 41 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 82 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 0.0170 chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN E 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.034519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.026575 restraints weight = 95047.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.027487 restraints weight = 54354.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.028159 restraints weight = 37247.324| |-----------------------------------------------------------------------------| r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12901 Z= 0.121 Angle : 0.595 9.583 17582 Z= 0.298 Chirality : 0.043 0.232 1985 Planarity : 0.003 0.031 2239 Dihedral : 7.376 59.794 2328 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.92 % Favored : 91.95 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1566 helix: 2.91 (0.26), residues: 402 sheet: -1.19 (0.34), residues: 204 loop : -2.26 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 255 HIS 0.004 0.001 HIS C 130 PHE 0.015 0.001 PHE E 115 TYR 0.026 0.001 TYR E 195 ARG 0.002 0.000 ARG D 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 15) link_NAG-ASN : angle 1.66964 ( 45) link_BETA1-4 : bond 0.00455 ( 13) link_BETA1-4 : angle 1.33303 ( 39) hydrogen bonds : bond 0.05226 ( 444) hydrogen bonds : angle 4.27087 ( 1239) link_BETA1-6 : bond 0.00564 ( 3) link_BETA1-6 : angle 1.10453 ( 9) SS BOND : bond 0.00279 ( 18) SS BOND : angle 1.20934 ( 36) covalent geometry : bond 0.00256 (12852) covalent geometry : angle 0.58457 (17453) ********************** 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 53 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8712 (mtp) cc_final: 0.8349 (mtp) REVERT: A 317 MET cc_start: 0.9140 (tmm) cc_final: 0.8490 (tmm) REVERT: B 27 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8911 (tm-30) REVERT: B 62 GLN cc_start: 0.9061 (pt0) cc_final: 0.8757 (pp30) REVERT: B 140 PHE cc_start: 0.8879 (m-80) cc_final: 0.8652 (m-80) REVERT: C 164 LEU cc_start: 0.9327 (tp) cc_final: 0.8935 (mt) REVERT: C 230 MET cc_start: 0.8853 (mtp) cc_final: 0.8541 (mtp) REVERT: C 317 MET cc_start: 0.8843 (tmm) cc_final: 0.8350 (tmm) REVERT: D 59 MET cc_start: 0.8760 (tpt) cc_final: 0.8502 (tpp) REVERT: D 140 PHE cc_start: 0.9319 (m-80) cc_final: 0.8889 (m-80) REVERT: E 115 PHE cc_start: 0.8432 (m-80) cc_final: 0.8211 (m-10) REVERT: E 317 MET cc_start: 0.9068 (tmm) cc_final: 0.8435 (tmm) REVERT: F 62 GLN cc_start: 0.9013 (pt0) cc_final: 0.8174 (pm20) REVERT: F 109 ASP cc_start: 0.8738 (m-30) cc_final: 0.8503 (m-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2050 time to fit residues: 18.1821 Evaluate side-chains 41 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 30 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.2777 r_free = 0.2777 target = 0.034581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.026659 restraints weight = 95332.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.027585 restraints weight = 54567.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.028260 restraints weight = 37140.335| |-----------------------------------------------------------------------------| r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12901 Z= 0.116 Angle : 0.582 9.584 17582 Z= 0.290 Chirality : 0.043 0.231 1985 Planarity : 0.003 0.031 2239 Dihedral : 7.254 59.965 2328 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.73 % Favored : 92.15 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1566 helix: 3.03 (0.25), residues: 399 sheet: -1.09 (0.35), residues: 204 loop : -2.21 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 255 HIS 0.004 0.001 HIS C 130 PHE 0.019 0.002 PHE C 258 TYR 0.021 0.001 TYR F 22 ARG 0.002 0.000 ARG D 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 15) link_NAG-ASN : angle 1.63979 ( 45) link_BETA1-4 : bond 0.00459 ( 13) link_BETA1-4 : angle 1.31435 ( 39) hydrogen bonds : bond 0.05051 ( 444) hydrogen bonds : angle 4.23392 ( 1239) link_BETA1-6 : bond 0.00560 ( 3) link_BETA1-6 : angle 1.10644 ( 9) SS BOND : bond 0.00267 ( 18) SS BOND : angle 1.15788 ( 36) covalent geometry : bond 0.00245 (12852) covalent geometry : angle 0.57187 (17453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3304.07 seconds wall clock time: 59 minutes 55.41 seconds (3595.41 seconds total)