Starting phenix.real_space_refine on Sat Feb 17 01:43:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oci_12808/02_2024/7oci_12808_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oci_12808/02_2024/7oci_12808.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oci_12808/02_2024/7oci_12808_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oci_12808/02_2024/7oci_12808_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oci_12808/02_2024/7oci_12808_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oci_12808/02_2024/7oci_12808.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oci_12808/02_2024/7oci_12808.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oci_12808/02_2024/7oci_12808_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oci_12808/02_2024/7oci_12808_updated.pdb" } resolution = 3.46 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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 11237 2.51 5 N 2663 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17077 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3503 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 869 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 104} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 933 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "E" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 5130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5130 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 615} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3177 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 376} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1873 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 15, 'TRANS': 242} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "K" 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'AJP': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'AJP': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 19 Chain: "F" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {' MG': 1, 'PEE': 1, 'V8K': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "G" 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: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 9.18, per 1000 atoms: 0.54 Number of scatterers: 17077 At special positions: 0 Unit cell: (152.04, 110.88, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 7 15.00 Mg 1 11.99 O 3114 8.00 N 2663 7.00 C 11237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1302 " - " ASN A 400 " " NAG G 501 " - " ASN G 332 " " NAG G 502 " - " ASN G 60 " " NAG J 1 " - " ASN F 539 " " NAG K 1 " - " ASN A 336 " Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 2.9 seconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 17 sheets defined 41.2% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.670A pdb=" N SER A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 443 through 446 No H-bonds generated for 'chain 'A' and resid 443 through 446' Processing helix chain 'A' and resid 448 through 469 removed outlier: 3.858A pdb=" N ILE A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 40 removed outlier: 3.791A pdb=" N ARG B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 67 removed outlier: 4.254A pdb=" N LEU B 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE B 47 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP B 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR B 49 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE B 52 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE B 53 " --> pdb=" O PHE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.702A pdb=" N ILE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 129 removed outlier: 3.579A pdb=" N PHE B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 129 " --> pdb=" O CYS B 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 231 removed outlier: 3.774A pdb=" N ILE C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Proline residue: C 229 - end of helix Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 265 through 290 removed outlier: 3.796A pdb=" N PHE C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 296 through 324 removed outlier: 4.224A pdb=" N ILE C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS C 324 " --> pdb=" O CYS C 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 32 removed outlier: 3.700A pdb=" N VAL D 23 " --> pdb=" O MET D 19 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 removed outlier: 3.851A pdb=" N HIS E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 48 removed outlier: 4.011A pdb=" N VAL E 35 " --> pdb=" O CYS E 31 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 43 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 82 removed outlier: 4.481A pdb=" N LEU E 63 " --> pdb=" O PHE E 59 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE E 66 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 30 removed outlier: 3.747A pdb=" N PHE F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 37 No H-bonds generated for 'chain 'F' and resid 34 through 37' Processing helix chain 'F' and resid 46 through 60 removed outlier: 4.450A pdb=" N PHE F 50 " --> pdb=" O PHE F 46 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 90 through 103 Processing helix chain 'F' and resid 111 through 137 removed outlier: 4.816A pdb=" N ALA F 119 " --> pdb=" O CYS F 115 " (cutoff:3.500A) Proline residue: F 120 - end of helix removed outlier: 3.987A pdb=" N GLY F 124 " --> pdb=" O PRO F 120 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR F 126 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE F 137 " --> pdb=" O PHE F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 removed outlier: 4.122A pdb=" N LEU F 144 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU F 145 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA F 151 " --> pdb=" O GLY F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 159 removed outlier: 4.987A pdb=" N ARG F 159 " --> pdb=" O GLY F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 188 removed outlier: 4.909A pdb=" N ILE F 172 " --> pdb=" O ALA F 169 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR F 173 " --> pdb=" O ILE F 170 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU F 174 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR F 178 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS F 187 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR F 188 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 207 removed outlier: 3.642A pdb=" N CYS F 196 " --> pdb=" O MET F 192 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA F 197 " --> pdb=" O HIS F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 227 Proline residue: F 219 - end of helix Processing helix chain 'F' and resid 233 through 252 removed outlier: 4.036A pdb=" N SER F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 262 No H-bonds generated for 'chain 'F' and resid 259 through 262' Processing helix chain 'F' and resid 266 through 288 removed outlier: 4.111A pdb=" N ALA F 280 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 361 Processing helix chain 'F' and resid 366 through 379 Proline residue: F 371 - end of helix Processing helix chain 'F' and resid 383 through 401 removed outlier: 3.830A pdb=" N PHE F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 429 removed outlier: 4.237A pdb=" N LEU F 407 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F 408 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Proline residue: F 411 - end of helix removed outlier: 3.833A pdb=" N VAL F 415 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER F 416 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA F 418 " --> pdb=" O VAL F 415 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL F 419 " --> pdb=" O SER F 416 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER F 422 " --> pdb=" O VAL F 419 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS F 423 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 472 removed outlier: 3.990A pdb=" N ALA F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER F 454 " --> pdb=" O ILE F 450 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE F 455 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP F 468 " --> pdb=" O PHE F 464 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR F 470 " --> pdb=" O SER F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 506 Processing helix chain 'F' and resid 520 through 525 Processing helix chain 'F' and resid 540 through 551 removed outlier: 3.807A pdb=" N VAL F 546 " --> pdb=" O HIS F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 560 removed outlier: 3.997A pdb=" N GLU F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 595 Processing helix chain 'F' and resid 604 through 607 No H-bonds generated for 'chain 'F' and resid 604 through 607' Processing helix chain 'F' and resid 628 through 633 Processing helix chain 'F' and resid 637 through 640 No H-bonds generated for 'chain 'F' and resid 637 through 640' Processing helix chain 'F' and resid 692 through 700 Processing helix chain 'G' and resid 37 through 50 removed outlier: 4.076A pdb=" N SER G 41 " --> pdb=" O GLU G 38 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL G 42 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR G 43 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS G 45 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN G 49 " --> pdb=" O ASP G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 93 removed outlier: 4.061A pdb=" N ALA G 91 " --> pdb=" O GLY G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 removed outlier: 3.785A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 129 Processing helix chain 'G' and resid 155 through 157 No H-bonds generated for 'chain 'G' and resid 155 through 157' Processing helix chain 'G' and resid 212 through 214 No H-bonds generated for 'chain 'G' and resid 212 through 214' Processing helix chain 'G' and resid 247 through 257 removed outlier: 3.683A pdb=" N LYS G 255 " --> pdb=" O LYS G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 394 through 413 removed outlier: 3.628A pdb=" N ALA G 398 " --> pdb=" O VAL G 394 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE G 399 " --> pdb=" O TYR G 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 128 removed outlier: 3.970A pdb=" N GLU H 125 " --> pdb=" O ALA H 121 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG H 128 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 215 removed outlier: 3.510A pdb=" N ILE H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 253 removed outlier: 3.623A pdb=" N GLU H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU H 253 " --> pdb=" O ALA H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 281 removed outlier: 3.554A pdb=" N LEU H 267 " --> pdb=" O SER H 263 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) Proline residue: H 270 - end of helix removed outlier: 3.782A pdb=" N LEU H 273 " --> pdb=" O ALA H 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 20 removed outlier: 3.951A pdb=" N UNK I 10 " --> pdb=" O UNK I 6 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 196 through 198 removed outlier: 4.299A pdb=" N PHE A 175 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR A 54 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 36 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU A 52 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG A 38 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A 50 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE A 40 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 80 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 66 through 70 Processing sheet with id= C, first strand: chain 'A' and resid 155 through 161 Processing sheet with id= D, first strand: chain 'A' and resid 400 through 406 removed outlier: 8.503A pdb=" N GLU A 378 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 236 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N SER A 380 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG A 238 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE A 382 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 240 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU A 256 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU A 236 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR A 254 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG A 238 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU A 252 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE A 240 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN A 250 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.505A pdb=" N HIS A 320 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 349 through 351 removed outlier: 6.563A pdb=" N ASP A 440 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE A 389 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 568 through 572 removed outlier: 6.170A pdb=" N GLN F 681 " --> pdb=" O GLU F 668 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLU F 668 " --> pdb=" O GLN F 681 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 645 through 647 Processing sheet with id= I, first strand: chain 'G' and resid 55 through 57 removed outlier: 3.501A pdb=" N VAL G 28 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN G 108 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL G 81 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU G 110 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 139 through 141 removed outlier: 3.586A pdb=" N VAL G 139 " --> pdb=" O GLU G 201 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 151 through 154 Processing sheet with id= L, first strand: chain 'G' and resid 263 through 266 removed outlier: 3.920A pdb=" N VAL G 263 " --> pdb=" O TRP G 299 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR G 340 " --> pdb=" O PRO G 329 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 269 through 273 Processing sheet with id= N, first strand: chain 'G' and resid 297 through 299 Processing sheet with id= O, first strand: chain 'G' and resid 367 through 375 removed outlier: 3.631A pdb=" N ASP G 369 " --> pdb=" O THR G 357 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR G 357 " --> pdb=" O ASP G 369 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP G 358 " --> pdb=" O GLN G 313 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN G 313 " --> pdb=" O ASP G 358 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 67 through 71 removed outlier: 3.806A pdb=" N GLN H 67 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY H 33 " --> pdb=" O GLN H 67 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 92 through 97 removed outlier: 6.624A pdb=" N LEU H 137 " --> pdb=" O GLU H 153 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU H 153 " --> pdb=" O LEU H 137 " (cutoff:3.500A) 689 hydrogen bonds defined for protein. 1791 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: 4.66 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2618 1.32 - 1.45: 5153 1.45 - 1.58: 9648 1.58 - 1.72: 14 1.72 - 1.85: 93 Bond restraints: 17526 Sorted by residual: bond pdb=" C45 V8K F 903 " pdb=" C46 V8K F 903 " ideal model delta sigma weight residual 1.338 1.542 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" O56 V8K F 903 " pdb=" P57 V8K F 903 " ideal model delta sigma weight residual 1.655 1.851 -0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C30 PEE D 101 " pdb=" O3 PEE D 101 " ideal model delta sigma weight residual 1.327 1.436 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C30 PEE C1801 " pdb=" O3 PEE C1801 " ideal model delta sigma weight residual 1.327 1.434 -0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C30 PEE B 201 " pdb=" O3 PEE B 201 " ideal model delta sigma weight residual 1.327 1.434 -0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 17521 not shown) Histogram of bond angle deviations from ideal: 96.07 - 103.66: 233 103.66 - 111.26: 7390 111.26 - 118.85: 6551 118.85 - 126.45: 9347 126.45 - 134.04: 280 Bond angle restraints: 23801 Sorted by residual: angle pdb=" C46 V8K F 903 " pdb=" C47 V8K F 903 " pdb=" C48 V8K F 903 " ideal model delta sigma weight residual 74.48 116.87 -42.39 3.00e+00 1.11e-01 2.00e+02 angle pdb=" C36 V8K F 903 " pdb=" C37 V8K F 903 " pdb=" C38 V8K F 903 " ideal model delta sigma weight residual 74.51 116.17 -41.66 3.00e+00 1.11e-01 1.93e+02 angle pdb=" C21 V8K F 903 " pdb=" C22 V8K F 903 " pdb=" C23 V8K F 903 " ideal model delta sigma weight residual 74.51 116.04 -41.53 3.00e+00 1.11e-01 1.92e+02 angle pdb=" C01 V8K F 903 " pdb=" C02 V8K F 903 " pdb=" C03 V8K F 903 " ideal model delta sigma weight residual 74.50 115.36 -40.86 3.00e+00 1.11e-01 1.86e+02 angle pdb=" C26 V8K F 903 " pdb=" C27 V8K F 903 " pdb=" C28 V8K F 903 " ideal model delta sigma weight residual 74.53 115.34 -40.81 3.00e+00 1.11e-01 1.85e+02 ... (remaining 23796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.66: 10200 34.66 - 69.32: 254 69.32 - 103.98: 45 103.98 - 138.64: 112 138.64 - 173.30: 15 Dihedral angle restraints: 10626 sinusoidal: 4480 harmonic: 6146 Sorted by residual: dihedral pdb=" CA TRP F 75 " pdb=" C TRP F 75 " pdb=" N TYR F 76 " pdb=" CA TYR F 76 " ideal model delta harmonic sigma weight residual -180.00 -152.39 -27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" C12 AJP B 202 " pdb=" C10 AJP B 202 " pdb=" C11 AJP B 202 " pdb=" O82 AJP B 202 " ideal model delta sinusoidal sigma weight residual 287.38 114.08 173.30 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C32 PEE C1801 " pdb=" C30 PEE C1801 " pdb=" C31 PEE C1801 " pdb=" O3 PEE C1801 " ideal model delta sinusoidal sigma weight residual 161.16 -30.48 -168.36 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 10623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.191: 2677 1.191 - 2.382: 0 2.382 - 3.573: 0 3.573 - 4.764: 9 4.764 - 5.954: 28 Chirality restraints: 2714 Sorted by residual: chirality pdb=" C12 AJP B 202 " pdb=" C07 AJP B 202 " pdb=" C11 AJP B 202 " pdb=" C13 AJP B 202 " both_signs ideal model delta sigma weight residual False 3.01 -2.95 5.95 2.00e-01 2.50e+01 8.86e+02 chirality pdb=" C12 AJP D 102 " pdb=" C07 AJP D 102 " pdb=" C11 AJP D 102 " pdb=" C13 AJP D 102 " both_signs ideal model delta sigma weight residual False 3.01 -2.87 5.88 2.00e-01 2.50e+01 8.64e+02 chirality pdb=" C20 AJP B 202 " pdb=" C15 AJP B 202 " pdb=" C19 AJP B 202 " pdb=" C21 AJP B 202 " both_signs ideal model delta sigma weight residual False 2.96 -2.90 5.86 2.00e-01 2.50e+01 8.58e+02 ... (remaining 2711 not shown) Planarity restraints: 2926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C44 V8K F 903 " -0.066 2.00e-02 2.50e+03 6.64e-02 4.41e+01 pdb=" C45 V8K F 903 " 0.063 2.00e-02 2.50e+03 pdb=" C46 V8K F 903 " 0.070 2.00e-02 2.50e+03 pdb=" C47 V8K F 903 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 145 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO H 146 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO H 146 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO H 146 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 426 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C ASP F 426 " -0.050 2.00e-02 2.50e+03 pdb=" O ASP F 426 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE F 427 " 0.017 2.00e-02 2.50e+03 ... (remaining 2923 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 440 2.70 - 3.25: 16923 3.25 - 3.80: 25083 3.80 - 4.35: 32713 4.35 - 4.90: 57000 Nonbonded interactions: 132159 Sorted by model distance: nonbonded pdb=" OD2 ASP D 29 " pdb=" OG SER F 141 " model vdw 2.155 2.440 nonbonded pdb=" OE2 GLU A 378 " pdb=" OG1 THR A 420 " model vdw 2.186 2.440 nonbonded pdb=" O LYS H 77 " pdb=" OG SER H 141 " model vdw 2.191 2.440 nonbonded pdb=" O GLY F 580 " pdb=" ND2 ASN F 585 " model vdw 2.234 2.520 nonbonded pdb=" OG1 THR H 136 " pdb=" O ARG H 152 " model vdw 2.263 2.440 ... (remaining 132154 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 3.920 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: 12.860 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 44.000 Find NCS groups from input model: 0.430 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.006 0.204 17526 Z= 0.406 Angle : 1.261 42.393 23801 Z= 0.479 Chirality : 0.592 5.954 2714 Planarity : 0.006 0.084 2921 Dihedral : 23.119 173.300 6658 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -2.61 (0.17), residues: 2047 helix: -0.90 (0.17), residues: 829 sheet: -1.95 (0.24), residues: 400 loop : -2.36 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 598 HIS 0.005 0.001 HIS F 465 PHE 0.018 0.001 PHE F 223 TYR 0.030 0.001 TYR F 391 ARG 0.005 0.000 ARG F 619 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.655 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.8375 (ptp) cc_final: 0.8084 (ptp) REVERT: F 528 ASP cc_start: 0.8506 (t0) cc_final: 0.8198 (t0) REVERT: F 548 LYS cc_start: 0.8832 (tttt) cc_final: 0.8592 (tttp) REVERT: G 57 LEU cc_start: 0.8663 (tp) cc_final: 0.8387 (tt) REVERT: G 106 GLU cc_start: 0.8311 (mp0) cc_final: 0.7909 (mt-10) REVERT: G 171 ASP cc_start: 0.7989 (m-30) cc_final: 0.7417 (p0) REVERT: G 236 ASP cc_start: 0.8354 (t0) cc_final: 0.8140 (t0) REVERT: G 240 ASN cc_start: 0.8019 (p0) cc_final: 0.7772 (p0) REVERT: G 381 ASP cc_start: 0.7492 (t70) cc_final: 0.7048 (t0) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2902 time to fit residues: 132.8563 Evaluate side-chains 245 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 97 GLN G 242 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17526 Z= 0.317 Angle : 1.214 36.557 23801 Z= 0.463 Chirality : 0.103 2.392 2714 Planarity : 0.005 0.060 2921 Dihedral : 21.171 179.043 2985 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.37 % Allowed : 8.28 % Favored : 90.35 % 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: -1.97 (0.17), residues: 2047 helix: -0.31 (0.18), residues: 834 sheet: -1.66 (0.24), residues: 410 loop : -2.07 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 368 HIS 0.005 0.001 HIS A 416 PHE 0.020 0.002 PHE F 587 TYR 0.027 0.001 TYR F 391 ARG 0.005 0.000 ARG F 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 258 time to evaluate : 2.461 Fit side-chains REVERT: A 116 ILE cc_start: 0.8741 (mp) cc_final: 0.8487 (mm) REVERT: A 150 MET cc_start: 0.8542 (ptp) cc_final: 0.8204 (ptp) REVERT: F 528 ASP cc_start: 0.8572 (t0) cc_final: 0.8320 (t0) REVERT: F 548 LYS cc_start: 0.8826 (tttt) cc_final: 0.8612 (tttp) REVERT: G 171 ASP cc_start: 0.8013 (m-30) cc_final: 0.7404 (p0) REVERT: G 236 ASP cc_start: 0.8406 (t0) cc_final: 0.8151 (t0) REVERT: G 311 ASP cc_start: 0.7383 (t0) cc_final: 0.7166 (t0) REVERT: H 141 SER cc_start: 0.7308 (m) cc_final: 0.6793 (m) REVERT: H 153 GLU cc_start: 0.8346 (tt0) cc_final: 0.7740 (tm-30) outliers start: 24 outliers final: 17 residues processed: 269 average time/residue: 0.3136 time to fit residues: 130.2631 Evaluate side-chains 268 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 251 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN G 377 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17526 Z= 0.358 Angle : 1.196 36.002 23801 Z= 0.458 Chirality : 0.103 2.463 2714 Planarity : 0.004 0.050 2921 Dihedral : 20.247 179.685 2985 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.11 % Allowed : 10.79 % Favored : 87.10 % 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: -1.71 (0.18), residues: 2047 helix: -0.09 (0.18), residues: 836 sheet: -1.46 (0.25), residues: 410 loop : -1.98 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 368 HIS 0.005 0.001 HIS F 465 PHE 0.025 0.002 PHE F 587 TYR 0.028 0.002 TYR F 391 ARG 0.005 0.000 ARG F 625 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 250 time to evaluate : 1.867 Fit side-chains revert: symmetry clash REVERT: A 116 ILE cc_start: 0.8679 (mp) cc_final: 0.8382 (mm) REVERT: A 150 MET cc_start: 0.8637 (ptp) cc_final: 0.8218 (ptp) REVERT: F 528 ASP cc_start: 0.8600 (t0) cc_final: 0.8353 (t0) REVERT: F 548 LYS cc_start: 0.8763 (tttt) cc_final: 0.8527 (tttp) REVERT: G 171 ASP cc_start: 0.8086 (m-30) cc_final: 0.7443 (p0) REVERT: G 236 ASP cc_start: 0.8396 (t0) cc_final: 0.8083 (t0) REVERT: G 311 ASP cc_start: 0.7361 (t0) cc_final: 0.7139 (t0) outliers start: 37 outliers final: 32 residues processed: 269 average time/residue: 0.2781 time to fit residues: 114.4531 Evaluate side-chains 266 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 234 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 186 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN H 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17526 Z= 0.246 Angle : 1.164 35.329 23801 Z= 0.437 Chirality : 0.100 2.338 2714 Planarity : 0.004 0.045 2921 Dihedral : 19.586 178.237 2985 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.23 % Allowed : 13.01 % Favored : 84.76 % 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: -1.38 (0.18), residues: 2047 helix: 0.18 (0.18), residues: 835 sheet: -1.24 (0.26), residues: 403 loop : -1.82 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 368 HIS 0.004 0.001 HIS F 465 PHE 0.019 0.001 PHE F 587 TYR 0.021 0.001 TYR F 391 ARG 0.008 0.000 ARG F 619 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 245 time to evaluate : 1.856 Fit side-chains REVERT: A 116 ILE cc_start: 0.8671 (mp) cc_final: 0.8344 (mm) REVERT: A 150 MET cc_start: 0.8531 (ptp) cc_final: 0.8095 (ptp) REVERT: F 186 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8090 (tm-30) REVERT: F 378 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.7952 (t80) REVERT: F 528 ASP cc_start: 0.8637 (t0) cc_final: 0.8403 (t0) REVERT: F 548 LYS cc_start: 0.8737 (tttt) cc_final: 0.8501 (tttp) REVERT: G 97 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8095 (mmmt) REVERT: G 171 ASP cc_start: 0.8085 (m-30) cc_final: 0.7466 (p0) REVERT: H 141 SER cc_start: 0.7297 (m) cc_final: 0.7083 (m) REVERT: H 155 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7280 (mp) outliers start: 39 outliers final: 31 residues processed: 262 average time/residue: 0.2762 time to fit residues: 110.7186 Evaluate side-chains 265 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 232 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 240 ASN H 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17526 Z= 0.296 Angle : 1.176 35.559 23801 Z= 0.444 Chirality : 0.100 2.273 2714 Planarity : 0.004 0.046 2921 Dihedral : 19.229 179.480 2985 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.31 % Allowed : 13.64 % Favored : 83.05 % 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: -1.29 (0.18), residues: 2047 helix: 0.27 (0.18), residues: 827 sheet: -1.19 (0.26), residues: 405 loop : -1.78 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 368 HIS 0.004 0.001 HIS A 416 PHE 0.022 0.001 PHE F 587 TYR 0.023 0.001 TYR F 391 ARG 0.006 0.000 ARG F 625 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 243 time to evaluate : 2.088 Fit side-chains REVERT: A 116 ILE cc_start: 0.8642 (mp) cc_final: 0.8298 (mm) REVERT: A 134 LYS cc_start: 0.8021 (mttt) cc_final: 0.7670 (mtpt) REVERT: A 150 MET cc_start: 0.8605 (ptp) cc_final: 0.8161 (ptp) REVERT: F 378 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.7995 (t80) REVERT: F 528 ASP cc_start: 0.8668 (t0) cc_final: 0.8440 (t0) REVERT: F 548 LYS cc_start: 0.8756 (tttt) cc_final: 0.8479 (tttp) REVERT: G 97 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8090 (mmmt) REVERT: G 171 ASP cc_start: 0.8098 (m-30) cc_final: 0.7509 (p0) REVERT: G 382 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: H 155 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7333 (mp) outliers start: 58 outliers final: 41 residues processed: 273 average time/residue: 0.2935 time to fit residues: 123.8947 Evaluate side-chains 271 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 227 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain H residue 91 ASN Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 3.9990 chunk 177 optimal weight: 50.0000 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN G 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 17526 Z= 0.428 Angle : 1.210 36.070 23801 Z= 0.467 Chirality : 0.101 2.257 2714 Planarity : 0.004 0.045 2921 Dihedral : 19.217 179.923 2985 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.71 % Allowed : 14.84 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.18), residues: 2047 helix: 0.12 (0.18), residues: 836 sheet: -1.20 (0.27), residues: 400 loop : -1.85 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 368 HIS 0.006 0.001 HIS A 416 PHE 0.026 0.002 PHE F 587 TYR 0.025 0.002 TYR F 391 ARG 0.008 0.000 ARG F 619 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 242 time to evaluate : 1.696 Fit side-chains REVERT: A 129 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7945 (m) REVERT: A 134 LYS cc_start: 0.8050 (mttt) cc_final: 0.7678 (mtpt) REVERT: A 150 MET cc_start: 0.8736 (ptp) cc_final: 0.8359 (ptp) REVERT: F 378 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.7970 (t80) REVERT: F 528 ASP cc_start: 0.8720 (t0) cc_final: 0.8491 (t0) REVERT: F 548 LYS cc_start: 0.8822 (tttt) cc_final: 0.8507 (tttp) REVERT: G 35 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7122 (mm-30) REVERT: G 97 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8144 (mmmt) REVERT: G 171 ASP cc_start: 0.8111 (m-30) cc_final: 0.7554 (p0) REVERT: G 382 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: H 155 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7437 (mp) outliers start: 65 outliers final: 49 residues processed: 278 average time/residue: 0.2737 time to fit residues: 116.8691 Evaluate side-chains 293 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 240 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 382 GLU Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain H residue 91 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 281 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 0.0980 chunk 166 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 196 optimal weight: 0.0030 chunk 123 optimal weight: 0.6980 chunk 119 optimal weight: 0.0970 chunk 90 optimal weight: 0.7980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 156 ASN G 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17526 Z= 0.147 Angle : 1.145 34.622 23801 Z= 0.427 Chirality : 0.099 2.187 2714 Planarity : 0.004 0.043 2921 Dihedral : 18.670 179.797 2985 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.40 % Allowed : 16.21 % Favored : 81.39 % 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 (0.19), residues: 2047 helix: 0.59 (0.19), residues: 823 sheet: -0.98 (0.27), residues: 381 loop : -1.66 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 368 HIS 0.003 0.001 HIS F 221 PHE 0.015 0.001 PHE H 79 TYR 0.012 0.001 TYR A 303 ARG 0.008 0.000 ARG F 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 253 time to evaluate : 1.920 Fit side-chains REVERT: A 134 LYS cc_start: 0.8007 (mttt) cc_final: 0.7687 (mtpt) REVERT: A 150 MET cc_start: 0.8414 (ptp) cc_final: 0.8086 (ptp) REVERT: B 65 ILE cc_start: 0.8282 (tt) cc_final: 0.8066 (tt) REVERT: B 97 GLN cc_start: 0.8684 (tt0) cc_final: 0.8452 (tt0) REVERT: F 378 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.7939 (t80) REVERT: F 548 LYS cc_start: 0.8713 (tttt) cc_final: 0.8452 (tttp) REVERT: F 632 MET cc_start: 0.8727 (ttp) cc_final: 0.8183 (mtp) REVERT: G 35 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6951 (mm-30) REVERT: G 97 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8067 (mmmt) REVERT: G 171 ASP cc_start: 0.8070 (m-30) cc_final: 0.7539 (p0) REVERT: G 234 SER cc_start: 0.8811 (t) cc_final: 0.8334 (m) REVERT: H 155 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7377 (mp) outliers start: 42 outliers final: 29 residues processed: 275 average time/residue: 0.2672 time to fit residues: 114.5923 Evaluate side-chains 255 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 224 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 340 THR Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 154 optimal weight: 0.0050 chunk 178 optimal weight: 40.0000 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 95 GLN A 276 GLN G 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17526 Z= 0.193 Angle : 1.152 34.832 23801 Z= 0.431 Chirality : 0.099 2.167 2714 Planarity : 0.004 0.044 2921 Dihedral : 18.506 179.637 2985 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.00 % Allowed : 16.78 % Favored : 81.22 % 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 (0.18), residues: 2047 helix: 0.62 (0.19), residues: 825 sheet: -0.95 (0.27), residues: 390 loop : -1.73 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 368 HIS 0.003 0.001 HIS F 465 PHE 0.014 0.001 PHE F 587 TYR 0.016 0.001 TYR F 391 ARG 0.007 0.000 ARG F 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 228 time to evaluate : 1.881 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8020 (mttt) cc_final: 0.7673 (mtpt) REVERT: A 150 MET cc_start: 0.8474 (ptp) cc_final: 0.8106 (ptp) REVERT: B 57 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7348 (mp) REVERT: B 65 ILE cc_start: 0.8291 (tt) cc_final: 0.8075 (tt) REVERT: B 97 GLN cc_start: 0.8686 (tt0) cc_final: 0.8423 (tt0) REVERT: C 328 TYR cc_start: 0.9171 (t80) cc_final: 0.8949 (t80) REVERT: F 378 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.7959 (t80) REVERT: F 548 LYS cc_start: 0.8703 (tttt) cc_final: 0.8396 (tttp) REVERT: G 35 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6958 (mm-30) REVERT: G 97 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8071 (mmmt) REVERT: G 171 ASP cc_start: 0.8078 (m-30) cc_final: 0.7557 (p0) REVERT: H 155 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7359 (mp) outliers start: 35 outliers final: 28 residues processed: 246 average time/residue: 0.2804 time to fit residues: 105.4238 Evaluate side-chains 250 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 219 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 265 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 chunk 143 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 165 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 182 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17526 Z= 0.181 Angle : 1.146 34.561 23801 Z= 0.427 Chirality : 0.099 2.137 2714 Planarity : 0.004 0.044 2921 Dihedral : 18.263 179.870 2985 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.17 % Allowed : 16.84 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.19), residues: 2047 helix: 0.71 (0.19), residues: 825 sheet: -0.88 (0.27), residues: 389 loop : -1.66 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 368 HIS 0.003 0.001 HIS F 465 PHE 0.012 0.001 PHE F 587 TYR 0.014 0.001 TYR F 391 ARG 0.007 0.000 ARG F 619 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 226 time to evaluate : 1.897 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8019 (mttt) cc_final: 0.7669 (mtpt) REVERT: A 150 MET cc_start: 0.8395 (ptp) cc_final: 0.8044 (ptp) REVERT: B 43 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8534 (mttt) REVERT: B 57 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7373 (mp) REVERT: B 65 ILE cc_start: 0.8243 (tt) cc_final: 0.8037 (tt) REVERT: B 97 GLN cc_start: 0.8695 (tt0) cc_final: 0.8413 (tt0) REVERT: C 328 TYR cc_start: 0.9163 (t80) cc_final: 0.8956 (t80) REVERT: F 378 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.7932 (t80) REVERT: F 548 LYS cc_start: 0.8683 (tttt) cc_final: 0.8387 (tttp) REVERT: G 35 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6934 (mm-30) REVERT: G 97 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8065 (mmmt) REVERT: G 171 ASP cc_start: 0.8085 (m-30) cc_final: 0.7537 (p0) REVERT: H 155 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7346 (mp) outliers start: 38 outliers final: 28 residues processed: 247 average time/residue: 0.2938 time to fit residues: 113.8878 Evaluate side-chains 247 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 216 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 265 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 203 optimal weight: 20.0000 chunk 187 optimal weight: 0.0670 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 128 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17526 Z= 0.178 Angle : 1.145 34.470 23801 Z= 0.426 Chirality : 0.099 2.126 2714 Planarity : 0.004 0.043 2921 Dihedral : 18.151 179.931 2985 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.00 % Allowed : 17.29 % Favored : 80.71 % 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: -0.80 (0.19), residues: 2047 helix: 0.76 (0.19), residues: 827 sheet: -0.86 (0.27), residues: 391 loop : -1.66 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 368 HIS 0.003 0.001 HIS F 465 PHE 0.012 0.001 PHE F 587 TYR 0.014 0.001 TYR F 391 ARG 0.007 0.000 ARG F 619 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 223 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8027 (mttt) cc_final: 0.7674 (mtpt) REVERT: A 150 MET cc_start: 0.8365 (ptp) cc_final: 0.8027 (ptp) REVERT: B 43 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8575 (mttt) REVERT: B 57 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7382 (mp) REVERT: C 239 MET cc_start: 0.7033 (mtt) cc_final: 0.6829 (mtt) REVERT: C 328 TYR cc_start: 0.9165 (t80) cc_final: 0.8963 (t80) REVERT: F 378 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.7940 (t80) REVERT: F 548 LYS cc_start: 0.8683 (tttt) cc_final: 0.8382 (tttp) REVERT: G 35 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6923 (mm-30) REVERT: G 97 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8061 (mmmt) REVERT: G 171 ASP cc_start: 0.8067 (m-30) cc_final: 0.7652 (p0) REVERT: H 99 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7411 (tm-30) REVERT: H 155 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7332 (mp) outliers start: 35 outliers final: 31 residues processed: 244 average time/residue: 0.2809 time to fit residues: 105.3594 Evaluate side-chains 252 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 218 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 671 THR Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 265 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 142 optimal weight: 0.0170 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.145538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.101166 restraints weight = 20191.797| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.20 r_work: 0.2727 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17526 Z= 0.151 Angle : 1.137 34.109 23801 Z= 0.421 Chirality : 0.098 2.108 2714 Planarity : 0.004 0.044 2921 Dihedral : 17.982 179.933 2985 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.88 % Allowed : 17.69 % Favored : 80.42 % 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: -0.67 (0.19), residues: 2047 helix: 0.88 (0.19), residues: 828 sheet: -0.78 (0.27), residues: 393 loop : -1.62 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 368 HIS 0.003 0.000 HIS F 221 PHE 0.010 0.001 PHE H 79 TYR 0.012 0.001 TYR F 391 ARG 0.006 0.000 ARG F 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3910.99 seconds wall clock time: 71 minutes 43.45 seconds (4303.45 seconds total)