Starting phenix.real_space_refine on Fri Mar 15 19:24:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjr_0237/03_2024/6hjr_0237.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjr_0237/03_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_0237/03_2024/6hjr_0237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjr_0237/03_2024/6hjr_0237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjr_0237/03_2024/6hjr_0237.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjr_0237/03_2024/6hjr_0237.pdb" } 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 Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.59, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 5.09 Conformation dependent library (CDL) restraints added in 2.1 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: 1.28 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: 3.57 Time building geometry restraints manager: 5.47 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: 98.15 - 105.36: 196 105.36 - 112.56: 6820 112.56 - 119.77: 4312 119.77 - 126.98: 5946 126.98 - 134.18: 179 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 2.440 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 2.440 nonbonded pdb=" O TYR D 141 " pdb=" ND2 ASN D 169 " model vdw 2.249 2.520 nonbonded pdb=" O LYS C 157 " pdb=" OG SER C 160 " model vdw 2.250 2.440 ... (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 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: 7.620 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: 29.900 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 33.920 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.410 ------------------------------------------------------------------------------- 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 : 1.468 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: 0.2836 time to fit residues: 42.4824 Evaluate side-chains 43 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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: 5.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 283 GLN A 286 HIS A 323 ASN C 108 GLN C 130 HIS C 226 GLN C 286 HIS E 108 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 ASN E 283 GLN F 53 ASN F 79 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12852 Z= 0.178 Angle : 0.672 9.834 17453 Z= 0.342 Chirality : 0.045 0.258 1985 Planarity : 0.004 0.037 2239 Dihedral : 10.720 69.132 2328 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.79 % Favored : 92.08 % Rotamer: Outliers : 0.15 % Allowed : 1.24 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.17 (0.19), residues: 1566 helix: 1.62 (0.24), residues: 397 sheet: -1.83 (0.32), residues: 204 loop : -2.90 (0.16), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 92 HIS 0.005 0.001 HIS C 276 PHE 0.037 0.002 PHE B 140 TYR 0.021 0.002 TYR F 190 ARG 0.006 0.000 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 81 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8578 (tmm) cc_final: 0.8354 (tmm) REVERT: B 62 GLN cc_start: 0.9020 (pt0) cc_final: 0.8551 (pm20) REVERT: B 109 ASP cc_start: 0.9066 (p0) cc_final: 0.8699 (m-30) REVERT: C 251 LEU cc_start: 0.9387 (tp) cc_final: 0.8991 (tt) REVERT: D 133 ILE cc_start: 0.9692 (pt) cc_final: 0.9321 (mm) REVERT: E 239 GLN cc_start: 0.9634 (pm20) cc_final: 0.8915 (pm20) REVERT: E 317 MET cc_start: 0.8961 (tmm) cc_final: 0.8403 (tmm) REVERT: F 62 GLN cc_start: 0.9041 (pt0) cc_final: 0.8416 (pm20) REVERT: F 122 VAL cc_start: 0.9584 (t) cc_final: 0.9306 (p) REVERT: F 125 GLN cc_start: 0.8611 (pt0) cc_final: 0.8106 (tt0) outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.2746 time to fit residues: 32.5669 Evaluate side-chains 46 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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: 6.9990 chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 113 optimal weight: 0.7980 overall best weight: 2.9784 ------------------------------------------------------------------------------- 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** A 283 GLN C 32 HIS C 130 HIS D 117 ASN E 32 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN F 169 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12852 Z= 0.294 Angle : 0.684 9.569 17453 Z= 0.350 Chirality : 0.045 0.247 1985 Planarity : 0.004 0.033 2239 Dihedral : 9.034 56.146 2328 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.45 % Favored : 90.42 % Rotamer: Outliers : 0.15 % Allowed : 1.86 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.77 (0.20), residues: 1566 helix: 2.14 (0.25), residues: 397 sheet: -1.60 (0.32), residues: 207 loop : -2.73 (0.17), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 153 HIS 0.011 0.002 HIS C 183 PHE 0.026 0.002 PHE C 115 TYR 0.023 0.002 TYR F 190 ARG 0.006 0.001 ARG F 75 *********************** 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 58 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8550 (m-80) cc_final: 0.8136 (m-80) REVERT: A 230 MET cc_start: 0.8725 (mtp) cc_final: 0.8252 (mtm) REVERT: A 317 MET cc_start: 0.8822 (tmm) cc_final: 0.8410 (tmm) REVERT: B 62 GLN cc_start: 0.9052 (pt0) cc_final: 0.8586 (pm20) REVERT: B 109 ASP cc_start: 0.9084 (p0) cc_final: 0.8773 (m-30) REVERT: D 133 ILE cc_start: 0.9702 (pt) cc_final: 0.9292 (mm) REVERT: D 140 PHE cc_start: 0.9152 (m-80) cc_final: 0.8592 (m-80) REVERT: D 149 MET cc_start: 0.9302 (mmp) cc_final: 0.9078 (mmm) REVERT: E 269 ILE cc_start: 0.9356 (mt) cc_final: 0.9105 (tt) REVERT: E 317 MET cc_start: 0.9037 (tmm) cc_final: 0.8411 (tmm) REVERT: F 62 GLN cc_start: 0.9043 (pt0) cc_final: 0.8438 (pm20) outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.2315 time to fit residues: 21.0498 Evaluate side-chains 40 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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: 6.9990 chunk 106 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 283 GLN A 323 ASN C 130 HIS D 117 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12852 Z= 0.171 Angle : 0.595 9.529 17453 Z= 0.304 Chirality : 0.043 0.241 1985 Planarity : 0.003 0.028 2239 Dihedral : 8.055 59.746 2328 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.73 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.20), residues: 1566 helix: 2.60 (0.25), residues: 394 sheet: -1.30 (0.32), residues: 213 loop : -2.58 (0.17), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 92 HIS 0.004 0.001 HIS E 276 PHE 0.014 0.002 PHE D 140 TYR 0.023 0.001 TYR F 190 ARG 0.004 0.000 ARG F 75 *********************** 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 62 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8442 (m-80) cc_final: 0.8165 (m-80) REVERT: A 317 MET cc_start: 0.8886 (tmm) cc_final: 0.8513 (tmm) REVERT: B 109 ASP cc_start: 0.9004 (p0) cc_final: 0.8710 (m-30) REVERT: B 140 PHE cc_start: 0.8697 (m-80) cc_final: 0.8398 (m-80) REVERT: C 109 LEU cc_start: 0.9716 (mm) cc_final: 0.9452 (tt) REVERT: C 230 MET cc_start: 0.9151 (mmm) cc_final: 0.8941 (mmm) REVERT: D 133 ILE cc_start: 0.9660 (pt) cc_final: 0.9220 (mm) REVERT: D 140 PHE cc_start: 0.9113 (m-80) cc_final: 0.8755 (m-80) REVERT: E 269 ILE cc_start: 0.9316 (mt) cc_final: 0.9094 (tt) REVERT: E 317 MET cc_start: 0.9004 (tmm) cc_final: 0.8473 (tmm) REVERT: F 62 GLN cc_start: 0.8995 (pt0) cc_final: 0.8383 (pm20) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2221 time to fit residues: 22.2400 Evaluate side-chains 44 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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: 0.8980 chunk 85 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 226 GLN A 283 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12852 Z= 0.382 Angle : 0.711 9.586 17453 Z= 0.364 Chirality : 0.045 0.238 1985 Planarity : 0.004 0.040 2239 Dihedral : 8.167 59.386 2328 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.92 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.50 (0.21), residues: 1566 helix: 2.34 (0.26), residues: 399 sheet: -1.33 (0.33), residues: 213 loop : -2.59 (0.18), residues: 954 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 0.016 0.002 PHE A 245 TYR 0.021 0.002 TYR F 190 ARG 0.008 0.001 ARG E 149 *********************** 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 55 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8630 (mtp) cc_final: 0.8327 (mtp) REVERT: A 317 MET cc_start: 0.9000 (tmm) cc_final: 0.8576 (tmm) REVERT: B 109 ASP cc_start: 0.9064 (p0) cc_final: 0.8818 (m-30) REVERT: B 140 PHE cc_start: 0.8763 (m-80) cc_final: 0.8496 (m-80) REVERT: C 109 LEU cc_start: 0.9737 (mm) cc_final: 0.9518 (tt) REVERT: C 230 MET cc_start: 0.9082 (mmm) cc_final: 0.8773 (mmm) REVERT: D 118 LEU cc_start: 0.9531 (tp) cc_final: 0.9326 (tt) REVERT: D 133 ILE cc_start: 0.9661 (pt) cc_final: 0.9352 (mm) REVERT: D 140 PHE cc_start: 0.9271 (m-80) cc_final: 0.8915 (m-80) REVERT: E 317 MET cc_start: 0.9085 (tmm) cc_final: 0.8460 (tmm) REVERT: F 62 GLN cc_start: 0.9025 (pt0) cc_final: 0.8387 (pm20) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2252 time to fit residues: 19.7623 Evaluate side-chains 40 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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: 50.0000 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 150 optimal weight: 0.4980 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.0270 chunk 79 optimal weight: 9.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12852 Z= 0.138 Angle : 0.587 9.522 17453 Z= 0.296 Chirality : 0.043 0.238 1985 Planarity : 0.003 0.028 2239 Dihedral : 7.681 58.955 2328 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.22 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (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: -1.11 (0.21), residues: 1566 helix: 2.85 (0.26), residues: 397 sheet: -1.22 (0.34), residues: 204 loop : -2.38 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 255 HIS 0.004 0.001 HIS E 276 PHE 0.021 0.002 PHE E 115 TYR 0.020 0.001 TYR F 190 ARG 0.004 0.000 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8605 (mtp) cc_final: 0.8339 (mtp) REVERT: A 317 MET cc_start: 0.8999 (tmm) cc_final: 0.8490 (tmm) REVERT: B 109 ASP cc_start: 0.8978 (p0) cc_final: 0.8697 (m-30) REVERT: B 140 PHE cc_start: 0.8642 (m-80) cc_final: 0.8332 (m-80) REVERT: B 149 MET cc_start: 0.8882 (mmt) cc_final: 0.8658 (mmt) REVERT: C 164 LEU cc_start: 0.9068 (tp) cc_final: 0.8657 (mt) REVERT: C 230 MET cc_start: 0.9083 (mmm) cc_final: 0.8867 (mmm) REVERT: D 118 LEU cc_start: 0.9482 (tp) cc_final: 0.9255 (tt) REVERT: D 133 ILE cc_start: 0.9651 (pt) cc_final: 0.9233 (mm) REVERT: D 140 PHE cc_start: 0.9062 (m-80) cc_final: 0.8739 (m-80) REVERT: E 317 MET cc_start: 0.9007 (tmm) cc_final: 0.8471 (tmm) REVERT: F 62 GLN cc_start: 0.8987 (pt0) cc_final: 0.8363 (pm20) REVERT: F 109 ASP cc_start: 0.8743 (m-30) cc_final: 0.8463 (p0) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2149 time to fit residues: 20.4499 Evaluate side-chains 42 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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: 5.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS C 130 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12852 Z= 0.200 Angle : 0.591 9.570 17453 Z= 0.300 Chirality : 0.043 0.234 1985 Planarity : 0.003 0.028 2239 Dihedral : 7.553 59.445 2328 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.88 % Favored : 91.00 % 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 : 0.07 % 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: -1.10 (0.21), residues: 1566 helix: 2.76 (0.26), residues: 401 sheet: -1.14 (0.34), residues: 204 loop : -2.36 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 255 HIS 0.005 0.001 HIS E 276 PHE 0.017 0.002 PHE E 115 TYR 0.019 0.001 TYR F 190 ARG 0.003 0.000 ARG D 116 *********************** 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 52 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8724 (mtp) cc_final: 0.8434 (mtp) REVERT: A 317 MET cc_start: 0.9056 (tmm) cc_final: 0.8570 (tmm) REVERT: B 149 MET cc_start: 0.8879 (mmt) cc_final: 0.8643 (mmt) REVERT: C 230 MET cc_start: 0.8983 (mmm) cc_final: 0.8736 (mmm) REVERT: D 118 LEU cc_start: 0.9483 (tp) cc_final: 0.9249 (tt) REVERT: D 133 ILE cc_start: 0.9639 (pt) cc_final: 0.9247 (mm) REVERT: D 140 PHE cc_start: 0.9192 (m-80) cc_final: 0.8865 (m-80) REVERT: E 317 MET cc_start: 0.9050 (tmm) cc_final: 0.8501 (tmm) REVERT: F 62 GLN cc_start: 0.8955 (pt0) cc_final: 0.8276 (pm20) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2678 time to fit residues: 23.3829 Evaluate side-chains 40 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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: 9.9990 chunk 89 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 102 optimal weight: 30.0000 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12852 Z= 0.425 Angle : 0.750 9.566 17453 Z= 0.381 Chirality : 0.045 0.237 1985 Planarity : 0.004 0.027 2239 Dihedral : 8.106 59.685 2328 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.49 % Favored : 88.38 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (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: -1.49 (0.21), residues: 1566 helix: 2.18 (0.26), residues: 407 sheet: -1.29 (0.33), residues: 213 loop : -2.55 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 255 HIS 0.009 0.002 HIS A 183 PHE 0.017 0.002 PHE A 245 TYR 0.019 0.002 TYR F 24 ARG 0.011 0.001 ARG F 106 *********************** 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 51 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8642 (mtp) cc_final: 0.8306 (mtp) REVERT: A 317 MET cc_start: 0.9036 (tmm) cc_final: 0.8590 (tmm) REVERT: C 164 LEU cc_start: 0.9216 (tp) cc_final: 0.8868 (mt) REVERT: C 317 MET cc_start: 0.8382 (tmm) cc_final: 0.8177 (tmm) REVERT: D 133 ILE cc_start: 0.9654 (pt) cc_final: 0.9343 (mm) REVERT: D 140 PHE cc_start: 0.9227 (m-80) cc_final: 0.9014 (m-80) REVERT: E 317 MET cc_start: 0.9087 (tmm) cc_final: 0.8405 (tmm) REVERT: F 62 GLN cc_start: 0.9052 (pt0) cc_final: 0.8349 (pm20) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2445 time to fit residues: 19.8016 Evaluate side-chains 37 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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: 0.9990 chunk 140 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 283 GLN B 62 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN F 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12852 Z= 0.156 Angle : 0.601 9.592 17453 Z= 0.305 Chirality : 0.043 0.238 1985 Planarity : 0.003 0.026 2239 Dihedral : 7.655 59.621 2328 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.60 % Favored : 92.27 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 2.69 (0.26), residues: 401 sheet: -1.15 (0.34), residues: 204 loop : -2.25 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 255 HIS 0.004 0.001 HIS E 183 PHE 0.009 0.001 PHE A 245 TYR 0.018 0.001 TYR F 190 ARG 0.003 0.000 ARG F 75 *********************** 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 54 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8565 (mtp) cc_final: 0.8315 (mtp) REVERT: A 317 MET cc_start: 0.9059 (tmm) cc_final: 0.8523 (tmm) REVERT: C 164 LEU cc_start: 0.9106 (tp) cc_final: 0.8766 (mt) REVERT: D 133 ILE cc_start: 0.9639 (pt) cc_final: 0.9228 (mm) REVERT: E 317 MET cc_start: 0.9041 (tmm) cc_final: 0.8459 (tmm) REVERT: F 62 GLN cc_start: 0.8999 (pt0) cc_final: 0.8319 (pm20) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2282 time to fit residues: 19.7315 Evaluate side-chains 40 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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: 4.9990 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 102 optimal weight: 0.0770 chunk 155 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 overall best weight: 2.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12852 Z= 0.246 Angle : 0.621 9.606 17453 Z= 0.316 Chirality : 0.044 0.231 1985 Planarity : 0.003 0.027 2239 Dihedral : 7.648 59.714 2328 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.13 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (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: 2.68 (0.26), residues: 402 sheet: -1.13 (0.34), residues: 204 loop : -2.25 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 255 HIS 0.005 0.001 HIS A 183 PHE 0.031 0.002 PHE B 140 TYR 0.018 0.001 TYR F 190 ARG 0.002 0.000 ARG A 212 ********************** 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 51 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8669 (mtp) cc_final: 0.8394 (mtp) REVERT: A 317 MET cc_start: 0.9092 (tmm) cc_final: 0.8618 (tmm) REVERT: C 164 LEU cc_start: 0.9131 (tp) cc_final: 0.8806 (mt) REVERT: E 317 MET cc_start: 0.9035 (tmm) cc_final: 0.8450 (tmm) REVERT: F 17 MET cc_start: 0.8848 (tpt) cc_final: 0.8587 (tpt) REVERT: F 62 GLN cc_start: 0.8996 (pt0) cc_final: 0.8249 (pm20) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2385 time to fit residues: 19.6512 Evaluate side-chains 39 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.477 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.033397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.025456 restraints weight = 100175.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.026330 restraints weight = 58623.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.026962 restraints weight = 41009.057| |-----------------------------------------------------------------------------| r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12852 Z= 0.413 Angle : 0.740 9.603 17453 Z= 0.377 Chirality : 0.045 0.214 1985 Planarity : 0.003 0.026 2239 Dihedral : 7.948 59.689 2328 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.24 % Favored : 88.63 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (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: 2.12 (0.26), residues: 408 sheet: -1.36 (0.33), residues: 219 loop : -2.42 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 255 HIS 0.008 0.002 HIS A 183 PHE 0.032 0.002 PHE D 140 TYR 0.019 0.002 TYR D 162 ARG 0.004 0.001 ARG C 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2116.55 seconds wall clock time: 40 minutes 4.17 seconds (2404.17 seconds total)