Starting phenix.real_space_refine on Thu Sep 26 10:01:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjr_0237/09_2024/6hjr_0237.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjr_0237/09_2024/6hjr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjr_0237/09_2024/6hjr_0237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjr_0237/09_2024/6hjr_0237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjr_0237/09_2024/6hjr_0237.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjr_0237/09_2024/6hjr_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.81, per 1000 atoms: 0.78 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: 3.42 Conformation dependent library (CDL) restraints added in 2.3 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: 1.39 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: 3.44 Time building geometry restraints manager: 3.93 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: 0.010 Normalize map: mean=0, sd=1: 12.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 32.850 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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: 0.010 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: 49.330 ------------------------------------------------------------------------------- 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 12852 Z= 0.620 Angle : 1.129 10.213 17453 Z= 0.603 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 1.380 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: 0.2743 time to fit residues: 40.9177 Evaluate side-chains 43 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 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 12852 Z= 0.204 Angle : 0.689 9.914 17453 Z= 0.353 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8630 (tmm) cc_final: 0.8417 (tmm) REVERT: B 62 GLN cc_start: 0.9021 (pt0) cc_final: 0.8557 (pm20) REVERT: B 109 ASP cc_start: 0.9094 (p0) cc_final: 0.8754 (m-30) REVERT: C 7 ILE cc_start: 0.9542 (OUTLIER) cc_final: 0.9313 (mp) REVERT: C 251 LEU cc_start: 0.9412 (tp) cc_final: 0.9035 (tt) REVERT: D 120 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8382 (mp0) REVERT: D 133 ILE cc_start: 0.9638 (pt) cc_final: 0.9100 (mm) REVERT: E 239 GLN cc_start: 0.9645 (pm20) cc_final: 0.8942 (pm20) REVERT: E 317 MET cc_start: 0.8986 (tmm) cc_final: 0.8459 (tmm) REVERT: F 62 GLN cc_start: 0.9033 (pt0) cc_final: 0.8411 (pm20) outliers start: 2 outliers final: 0 residues processed: 76 average time/residue: 0.2587 time to fit residues: 29.1520 Evaluate side-chains 43 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 150 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS C 130 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12852 Z= 0.233 Angle : 0.641 9.578 17453 Z= 0.328 Chirality : 0.044 0.247 1985 Planarity : 0.003 0.034 2239 Dihedral : 8.929 58.042 2328 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.88 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -1.74 (0.20), residues: 1566 helix: 2.19 (0.25), residues: 392 sheet: -1.60 (0.32), residues: 207 loop : -2.69 (0.17), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 153 HIS 0.009 0.001 HIS C 183 PHE 0.026 0.002 PHE C 115 TYR 0.020 0.002 TYR F 190 ARG 0.004 0.000 ARG D 106 *********************** 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 59 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8849 (tmm) cc_final: 0.8488 (tmm) REVERT: B 62 GLN cc_start: 0.8998 (pt0) cc_final: 0.8551 (pm20) REVERT: B 109 ASP cc_start: 0.9031 (p0) cc_final: 0.8784 (m-30) REVERT: D 140 PHE cc_start: 0.8954 (m-80) cc_final: 0.8390 (m-80) REVERT: D 149 MET cc_start: 0.9324 (mmp) cc_final: 0.9097 (mmm) REVERT: E 269 ILE cc_start: 0.9380 (mt) cc_final: 0.9117 (tt) REVERT: E 317 MET cc_start: 0.9046 (tmm) cc_final: 0.8438 (tmm) REVERT: F 62 GLN cc_start: 0.9016 (pt0) cc_final: 0.8406 (pm20) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2232 time to fit residues: 21.0215 Evaluate side-chains 40 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 0.0570 chunk 67 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN C 130 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12852 Z= 0.371 Angle : 0.711 9.536 17453 Z= 0.363 Chirality : 0.045 0.250 1985 Planarity : 0.004 0.037 2239 Dihedral : 8.390 56.574 2328 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.22 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -1.61 (0.20), residues: 1566 helix: 2.35 (0.25), residues: 393 sheet: -1.56 (0.33), residues: 207 loop : -2.63 (0.17), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 255 HIS 0.008 0.002 HIS A 183 PHE 0.028 0.002 PHE B 140 TYR 0.017 0.002 TYR C 195 ARG 0.007 0.001 ARG E 149 *********************** 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 56 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8650 (mtp) cc_final: 0.8335 (mtp) REVERT: A 317 MET cc_start: 0.8995 (tmm) cc_final: 0.8549 (tmm) REVERT: B 62 GLN cc_start: 0.9041 (pt0) cc_final: 0.8772 (pp30) REVERT: B 140 PHE cc_start: 0.8783 (m-80) cc_final: 0.8489 (m-80) REVERT: C 230 MET cc_start: 0.9099 (mmm) cc_final: 0.8771 (mmm) REVERT: D 140 PHE cc_start: 0.9066 (m-80) cc_final: 0.8803 (m-80) REVERT: E 269 ILE cc_start: 0.9381 (mt) cc_final: 0.9153 (tt) REVERT: E 317 MET cc_start: 0.9095 (tmm) cc_final: 0.8465 (tmm) REVERT: F 62 GLN cc_start: 0.9018 (pt0) cc_final: 0.8338 (pm20) REVERT: F 109 ASP cc_start: 0.8914 (m-30) cc_final: 0.8397 (m-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2445 time to fit residues: 21.3640 Evaluate side-chains 38 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 0.0040 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 250 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12852 Z= 0.148 Angle : 0.586 9.526 17453 Z= 0.297 Chirality : 0.044 0.238 1985 Planarity : 0.003 0.032 2239 Dihedral : 7.752 56.104 2328 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.66 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: -1.28 (0.20), residues: 1566 helix: 2.68 (0.25), residues: 395 sheet: -1.34 (0.33), residues: 204 loop : -2.46 (0.17), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 255 HIS 0.004 0.001 HIS E 276 PHE 0.022 0.002 PHE B 140 TYR 0.017 0.001 TYR F 190 ARG 0.004 0.000 ARG F 106 *********************** 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 60 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8632 (mtp) cc_final: 0.8345 (mtp) REVERT: A 317 MET cc_start: 0.8981 (tmm) cc_final: 0.8582 (tmm) REVERT: B 27 GLN cc_start: 0.9190 (tm-30) cc_final: 0.8962 (tm-30) REVERT: B 62 GLN cc_start: 0.8944 (pt0) cc_final: 0.8473 (pm20) REVERT: B 140 PHE cc_start: 0.8594 (m-80) cc_final: 0.8232 (m-80) REVERT: C 164 LEU cc_start: 0.9135 (tp) cc_final: 0.8834 (mt) REVERT: D 140 PHE cc_start: 0.8907 (m-80) cc_final: 0.8436 (m-80) REVERT: E 269 ILE cc_start: 0.9367 (mt) cc_final: 0.9147 (tt) REVERT: E 317 MET cc_start: 0.9014 (tmm) cc_final: 0.8455 (tmm) REVERT: F 62 GLN cc_start: 0.8942 (pt0) cc_final: 0.8344 (pm20) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2275 time to fit residues: 21.8801 Evaluate side-chains 40 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 30.0000 chunk 135 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 0.0270 chunk 49 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 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 0.029 12852 Z= 0.202 Angle : 0.598 9.580 17453 Z= 0.304 Chirality : 0.044 0.248 1985 Planarity : 0.003 0.031 2239 Dihedral : 7.512 59.328 2328 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.98 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.19 (0.21), residues: 1566 helix: 2.73 (0.26), residues: 397 sheet: -1.31 (0.33), residues: 204 loop : -2.40 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 255 HIS 0.005 0.001 HIS E 276 PHE 0.019 0.002 PHE B 140 TYR 0.016 0.001 TYR F 190 ARG 0.003 0.000 ARG F 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8741 (mtp) cc_final: 0.8432 (mtp) REVERT: A 317 MET cc_start: 0.9023 (tmm) cc_final: 0.8536 (tmm) REVERT: B 17 MET cc_start: 0.8854 (tpp) cc_final: 0.8610 (tpp) REVERT: B 27 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8934 (tm-30) REVERT: B 140 PHE cc_start: 0.8593 (m-80) cc_final: 0.8341 (m-80) REVERT: C 164 LEU cc_start: 0.9178 (tp) cc_final: 0.8843 (mt) REVERT: D 140 PHE cc_start: 0.9008 (m-80) cc_final: 0.8562 (m-80) REVERT: E 269 ILE cc_start: 0.9399 (mt) cc_final: 0.9179 (tt) REVERT: E 317 MET cc_start: 0.9052 (tmm) cc_final: 0.8465 (tmm) REVERT: F 62 GLN cc_start: 0.8943 (pt0) cc_final: 0.8309 (pm20) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2355 time to fit residues: 21.6821 Evaluate side-chains 38 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12852 Z= 0.163 Angle : 0.571 9.542 17453 Z= 0.289 Chirality : 0.043 0.240 1985 Planarity : 0.003 0.032 2239 Dihedral : 7.297 58.701 2328 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.85 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.06 (0.21), residues: 1566 helix: 2.89 (0.25), residues: 397 sheet: -1.27 (0.33), residues: 204 loop : -2.32 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 255 HIS 0.005 0.001 HIS E 276 PHE 0.018 0.001 PHE A 115 TYR 0.016 0.001 TYR F 190 ARG 0.003 0.000 ARG D 106 *********************** 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 54 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8721 (mtp) cc_final: 0.8405 (mtp) REVERT: A 317 MET cc_start: 0.9030 (tmm) cc_final: 0.8577 (tmm) REVERT: B 27 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8972 (tm-30) REVERT: B 140 PHE cc_start: 0.8592 (m-80) cc_final: 0.8238 (m-80) REVERT: C 164 LEU cc_start: 0.9196 (tp) cc_final: 0.8834 (mt) REVERT: D 140 PHE cc_start: 0.9047 (m-80) cc_final: 0.8556 (m-80) REVERT: E 269 ILE cc_start: 0.9419 (mt) cc_final: 0.9211 (tt) REVERT: E 317 MET cc_start: 0.9023 (tmm) cc_final: 0.8468 (tmm) REVERT: F 62 GLN cc_start: 0.8913 (pt0) cc_final: 0.8285 (pm20) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2251 time to fit residues: 19.6097 Evaluate side-chains 40 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12852 Z= 0.326 Angle : 0.654 9.561 17453 Z= 0.331 Chirality : 0.044 0.239 1985 Planarity : 0.003 0.031 2239 Dihedral : 7.423 55.568 2328 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.03 % Favored : 89.85 % 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: -1.15 (0.21), residues: 1566 helix: 2.72 (0.26), residues: 405 sheet: -1.32 (0.34), residues: 204 loop : -2.37 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 255 HIS 0.006 0.002 HIS A 183 PHE 0.021 0.002 PHE B 140 TYR 0.016 0.002 TYR C 195 ARG 0.003 0.001 ARG A 212 *********************** 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 54 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8740 (mtp) cc_final: 0.8392 (mtp) REVERT: A 317 MET cc_start: 0.9076 (tmm) cc_final: 0.8607 (tmm) REVERT: B 27 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8959 (tm-30) REVERT: B 140 PHE cc_start: 0.8789 (m-80) cc_final: 0.8411 (m-80) REVERT: C 164 LEU cc_start: 0.9239 (tp) cc_final: 0.8839 (mt) REVERT: D 140 PHE cc_start: 0.9182 (m-80) cc_final: 0.8671 (m-80) REVERT: E 317 MET cc_start: 0.9054 (tmm) cc_final: 0.8388 (tmm) REVERT: F 62 GLN cc_start: 0.8963 (pt0) cc_final: 0.8204 (pm20) REVERT: F 109 ASP cc_start: 0.8703 (m-30) cc_final: 0.8493 (m-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2206 time to fit residues: 19.1739 Evaluate side-chains 37 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12852 Z= 0.203 Angle : 0.604 10.209 17453 Z= 0.306 Chirality : 0.043 0.234 1985 Planarity : 0.003 0.054 2239 Dihedral : 7.343 58.344 2328 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.11 % Favored : 91.76 % 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: -1.04 (0.21), residues: 1566 helix: 2.81 (0.26), residues: 405 sheet: -1.30 (0.34), residues: 204 loop : -2.30 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 255 HIS 0.006 0.001 HIS E 183 PHE 0.021 0.002 PHE B 140 TYR 0.015 0.001 TYR C 195 ARG 0.007 0.000 ARG D 127 *********************** 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 51 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8692 (mtp) cc_final: 0.8369 (mtp) REVERT: A 317 MET cc_start: 0.9068 (tmm) cc_final: 0.8614 (tmm) REVERT: B 27 GLN cc_start: 0.9227 (tm-30) cc_final: 0.8951 (tm-30) REVERT: B 140 PHE cc_start: 0.8742 (m-80) cc_final: 0.8350 (m-80) REVERT: C 164 LEU cc_start: 0.9221 (tp) cc_final: 0.8821 (mt) REVERT: D 140 PHE cc_start: 0.9120 (m-80) cc_final: 0.8694 (m-80) REVERT: E 317 MET cc_start: 0.9052 (tmm) cc_final: 0.8454 (tmm) REVERT: F 62 GLN cc_start: 0.8935 (pt0) cc_final: 0.8203 (pm20) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2104 time to fit residues: 18.1317 Evaluate side-chains 37 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12852 Z= 0.354 Angle : 0.695 9.599 17453 Z= 0.352 Chirality : 0.045 0.233 1985 Planarity : 0.003 0.040 2239 Dihedral : 7.529 55.734 2328 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.22 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.24 (0.21), residues: 1566 helix: 2.55 (0.25), residues: 405 sheet: -1.44 (0.34), residues: 204 loop : -2.37 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 255 HIS 0.008 0.002 HIS E 183 PHE 0.023 0.002 PHE B 140 TYR 0.017 0.002 TYR C 195 ARG 0.016 0.001 ARG F 116 ********************** 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 52 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8657 (mtp) cc_final: 0.8316 (mtp) REVERT: A 317 MET cc_start: 0.9069 (tmm) cc_final: 0.8618 (tmm) REVERT: B 27 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8947 (tm-30) REVERT: C 164 LEU cc_start: 0.9282 (tp) cc_final: 0.8889 (mt) REVERT: C 230 MET cc_start: 0.8904 (mmm) cc_final: 0.8697 (mmm) REVERT: D 140 PHE cc_start: 0.9187 (m-80) cc_final: 0.8857 (m-80) REVERT: E 317 MET cc_start: 0.9095 (tmm) cc_final: 0.8401 (tmm) REVERT: F 62 GLN cc_start: 0.8989 (pt0) cc_final: 0.8239 (pm20) REVERT: F 109 ASP cc_start: 0.8771 (m-30) cc_final: 0.8522 (m-30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1967 time to fit residues: 17.3468 Evaluate side-chains 37 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 15 optimal weight: 0.0060 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN F 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.034626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.026604 restraints weight = 95807.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.027542 restraints weight = 54878.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.028213 restraints weight = 37554.697| |-----------------------------------------------------------------------------| r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12852 Z= 0.151 Angle : 0.585 9.543 17453 Z= 0.296 Chirality : 0.043 0.230 1985 Planarity : 0.003 0.034 2239 Dihedral : 7.261 58.965 2328 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.22 % Favored : 92.66 % 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: 2.86 (0.26), residues: 402 sheet: -1.19 (0.35), residues: 204 loop : -2.24 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 255 HIS 0.003 0.001 HIS E 276 PHE 0.017 0.002 PHE E 115 TYR 0.018 0.001 TYR F 22 ARG 0.005 0.000 ARG D 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2082.21 seconds wall clock time: 38 minutes 56.67 seconds (2336.67 seconds total)