Starting phenix.real_space_refine on Thu Nov 14 21:50:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/11_2024/8gcm_29935_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/11_2024/8gcm_29935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/11_2024/8gcm_29935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/11_2024/8gcm_29935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/11_2024/8gcm_29935_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/11_2024/8gcm_29935_neut.cif" } resolution = 3.5 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= -0.002 sd= 0.060 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 C 4769 2.51 5 N 1295 2.21 5 O 1389 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7508 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1430 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 197} Chain breaks: 5 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'PHE%COO:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2384 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 156 Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 352 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1672 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1640 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 193 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'YX9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.66 Number of scatterers: 7508 At special positions: 0 Unit cell: (89.79, 119.355, 127.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 F 2 9.00 O 1389 8.00 N 1295 7.00 C 4769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 33.4% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 removed outlier: 4.622A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 removed outlier: 3.767A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.128A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.688A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.567A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.610A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.644A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.896A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 31 through 42 removed outlier: 4.177A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.616A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.656A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.630A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'R' and resid 24 through 45 removed outlier: 4.066A pdb=" N PHE R 28 " --> pdb=" O PRO R 24 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE R 29 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY R 31 " --> pdb=" O MET R 27 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL R 33 " --> pdb=" O ILE R 29 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 50 Processing helix chain 'R' and resid 54 through 72 removed outlier: 3.601A pdb=" N LEU R 70 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL R 72 " --> pdb=" O GLY R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 77 removed outlier: 3.967A pdb=" N THR R 76 " --> pdb=" O SER R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 106 removed outlier: 3.506A pdb=" N LEU R 99 " --> pdb=" O SER R 95 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU R 100 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 114 Processing helix chain 'R' and resid 115 through 120 Processing helix chain 'R' and resid 123 through 130 Processing helix chain 'R' and resid 134 through 156 removed outlier: 4.066A pdb=" N LEU R 138 " --> pdb=" O ARG R 134 " (cutoff:3.500A) Proline residue: R 154 - end of helix Processing helix chain 'R' and resid 184 through 219 removed outlier: 3.881A pdb=" N CYS R 207 " --> pdb=" O ASN R 203 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU R 211 " --> pdb=" O CYS R 207 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET R 218 " --> pdb=" O HIS R 214 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG R 219 " --> pdb=" O ARG R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 284 removed outlier: 3.639A pdb=" N VAL R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE R 272 " --> pdb=" O ILE R 268 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU R 273 " --> pdb=" O GLN R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 298 removed outlier: 4.112A pdb=" N VAL R 289 " --> pdb=" O SER R 285 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 319 removed outlier: 3.564A pdb=" N SER R 319 " --> pdb=" O ILE R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 325 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.918A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 221 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.918A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.017A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.005A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.687A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.607A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.801A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.708A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 removed outlier: 4.050A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.723A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.820A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 49 through 50 removed outlier: 3.920A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.660A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 204 " --> pdb=" O THR E 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.772A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 852 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: 2.15 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1223 1.26 - 1.40: 1952 1.40 - 1.54: 4323 1.54 - 1.68: 73 1.68 - 1.82: 76 Bond restraints: 7647 Sorted by residual: bond pdb=" C14 YX9 R 501 " pdb=" C18 YX9 R 501 " ideal model delta sigma weight residual 1.535 1.305 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C16 YX9 R 501 " pdb=" C17 YX9 R 501 " ideal model delta sigma weight residual 1.515 1.330 0.185 2.00e-02 2.50e+03 8.52e+01 bond pdb=" C14 YX9 R 501 " pdb=" N15 YX9 R 501 " ideal model delta sigma weight residual 1.458 1.598 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C17 YX9 R 501 " pdb=" C18 YX9 R 501 " ideal model delta sigma weight residual 1.525 1.665 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C16 YX9 R 501 " pdb=" N15 YX9 R 501 " ideal model delta sigma weight residual 1.349 1.475 -0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 7642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 10161 3.44 - 6.87: 239 6.87 - 10.31: 38 10.31 - 13.74: 4 13.74 - 17.18: 1 Bond angle restraints: 10443 Sorted by residual: angle pdb=" C SER R 73 " pdb=" N PRO R 74 " pdb=" CA PRO R 74 " ideal model delta sigma weight residual 119.19 136.37 -17.18 1.06e+00 8.90e-01 2.63e+02 angle pdb=" N ILE R 29 " pdb=" CA ILE R 29 " pdb=" C ILE R 29 " ideal model delta sigma weight residual 110.72 122.06 -11.34 1.01e+00 9.80e-01 1.26e+02 angle pdb=" N MET R 27 " pdb=" CA MET R 27 " pdb=" C MET R 27 " ideal model delta sigma weight residual 111.03 120.67 -9.64 1.11e+00 8.12e-01 7.54e+01 angle pdb=" C ILE R 23 " pdb=" N PRO R 24 " pdb=" CA PRO R 24 " ideal model delta sigma weight residual 119.84 130.45 -10.61 1.25e+00 6.40e-01 7.20e+01 angle pdb=" N ALA R 25 " pdb=" CA ALA R 25 " pdb=" C ALA R 25 " ideal model delta sigma weight residual 111.28 120.23 -8.95 1.09e+00 8.42e-01 6.74e+01 ... (remaining 10438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4062 18.00 - 36.00: 304 36.00 - 54.00: 63 54.00 - 71.99: 13 71.99 - 89.99: 8 Dihedral angle restraints: 4450 sinusoidal: 1332 harmonic: 3118 Sorted by residual: dihedral pdb=" CA PHE R 97 " pdb=" C PHE R 97 " pdb=" N ILE R 98 " pdb=" CA ILE R 98 " ideal model delta harmonic sigma weight residual -180.00 -151.65 -28.35 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CB CYS R 92 " pdb=" SG CYS R 92 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 44.83 48.17 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" C VAL R 306 " pdb=" N VAL R 306 " pdb=" CA VAL R 306 " pdb=" CB VAL R 306 " ideal model delta harmonic sigma weight residual -122.00 -135.79 13.79 0 2.50e+00 1.60e-01 3.04e+01 ... (remaining 4447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1106 0.098 - 0.197: 122 0.197 - 0.295: 21 0.295 - 0.393: 3 0.393 - 0.492: 3 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA VAL R 306 " pdb=" N VAL R 306 " pdb=" C VAL R 306 " pdb=" CB VAL R 306 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CA LYS B 280 " pdb=" N LYS B 280 " pdb=" C LYS B 280 " pdb=" CB LYS B 280 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA MET R 27 " pdb=" N MET R 27 " pdb=" C MET R 27 " pdb=" CB MET R 27 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1252 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 276 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C VAL B 276 " 0.069 2.00e-02 2.50e+03 pdb=" O VAL B 276 " -0.025 2.00e-02 2.50e+03 pdb=" N SER B 277 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 150 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C PHE R 150 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE R 150 " 0.022 2.00e-02 2.50e+03 pdb=" N CYS R 151 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 321 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO R 322 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO R 322 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 322 " 0.038 5.00e-02 4.00e+02 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1272 2.76 - 3.29: 6737 3.29 - 3.83: 11485 3.83 - 4.36: 12412 4.36 - 4.90: 22557 Nonbonded interactions: 54463 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.223 3.040 nonbonded pdb=" O GLU R 93 " pdb=" OG1 THR R 96 " model vdw 2.284 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.304 3.040 nonbonded pdb=" OG SER B 245 " pdb=" N ASP B 246 " model vdw 2.313 3.120 nonbonded pdb=" O SER R 114 " pdb=" OG SER R 114 " model vdw 2.357 3.040 ... (remaining 54458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.010 0.230 7647 Z= 0.666 Angle : 1.247 17.178 10443 Z= 0.784 Chirality : 0.072 0.492 1255 Planarity : 0.007 0.071 1330 Dihedral : 14.656 89.992 2424 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.77 % Allowed : 1.85 % Favored : 97.38 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.24), residues: 1047 helix: -0.78 (0.29), residues: 312 sheet: -2.82 (0.28), residues: 271 loop : -2.80 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 339 HIS 0.010 0.001 HIS E 35 PHE 0.026 0.003 PHE B 235 TYR 0.020 0.002 TYR B 85 ARG 0.018 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.831 Fit side-chains REVERT: B 17 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8119 (tm-30) REVERT: E 246 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7051 (mm-30) REVERT: R 117 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7452 (mtm110) REVERT: R 169 TRP cc_start: 0.6528 (p-90) cc_final: 0.6140 (p-90) REVERT: R 217 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5330 (t80) outliers start: 5 outliers final: 3 residues processed: 111 average time/residue: 0.2311 time to fit residues: 33.5120 Evaluate side-chains 89 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 217 PHE Chi-restraints excluded: chain R residue 315 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.0270 chunk 61 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN R 313 GLN R 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7647 Z= 0.147 Angle : 0.582 6.956 10443 Z= 0.310 Chirality : 0.042 0.145 1255 Planarity : 0.004 0.057 1330 Dihedral : 8.432 80.746 1171 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.62 % Allowed : 11.38 % Favored : 88.00 % 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: -2.60 (0.25), residues: 1047 helix: 0.16 (0.30), residues: 322 sheet: -2.51 (0.29), residues: 275 loop : -2.56 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.017 0.001 PHE R 126 TYR 0.015 0.001 TYR R 184 ARG 0.003 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7988 (tm-30) REVERT: B 222 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: E 246 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6980 (mm-30) REVERT: R 81 MET cc_start: 0.5859 (mmm) cc_final: 0.5561 (mmm) outliers start: 4 outliers final: 1 residues processed: 95 average time/residue: 0.2328 time to fit residues: 29.2829 Evaluate side-chains 82 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain B residue 222 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 85 optimal weight: 0.0030 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.9292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7647 Z= 0.189 Angle : 0.557 6.822 10443 Z= 0.297 Chirality : 0.042 0.146 1255 Planarity : 0.004 0.059 1330 Dihedral : 7.292 61.271 1165 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.69 % Allowed : 14.31 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.26), residues: 1047 helix: 0.65 (0.31), residues: 320 sheet: -2.22 (0.30), residues: 266 loop : -2.47 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.007 0.001 HIS B 225 PHE 0.016 0.001 PHE B 235 TYR 0.014 0.001 TYR R 184 ARG 0.003 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7957 (tm-30) REVERT: B 51 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7967 (mt) REVERT: B 222 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: E 246 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6912 (mm-30) REVERT: R 117 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7531 (mtm110) outliers start: 11 outliers final: 5 residues processed: 90 average time/residue: 0.2381 time to fit residues: 28.2815 Evaluate side-chains 85 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7647 Z= 0.202 Angle : 0.542 6.824 10443 Z= 0.290 Chirality : 0.042 0.141 1255 Planarity : 0.004 0.057 1330 Dihedral : 5.822 58.159 1163 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.15 % Allowed : 16.62 % Favored : 81.23 % 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: -1.94 (0.26), residues: 1047 helix: 0.92 (0.31), residues: 319 sheet: -2.16 (0.30), residues: 266 loop : -2.33 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.015 0.001 PHE B 235 TYR 0.014 0.001 TYR R 184 ARG 0.003 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.867 Fit side-chains REVERT: B 17 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7950 (tm-30) REVERT: B 51 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8148 (mt) REVERT: E 34 MET cc_start: 0.7315 (tpp) cc_final: 0.7027 (tpp) REVERT: E 38 ARG cc_start: 0.8260 (mtm180) cc_final: 0.8041 (mtp180) REVERT: E 231 GLN cc_start: 0.8152 (pp30) cc_final: 0.7742 (pp30) REVERT: E 246 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6945 (mm-30) REVERT: R 117 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7499 (mtm110) outliers start: 14 outliers final: 6 residues processed: 98 average time/residue: 0.2386 time to fit residues: 30.6212 Evaluate side-chains 88 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7647 Z= 0.368 Angle : 0.655 9.991 10443 Z= 0.348 Chirality : 0.045 0.193 1255 Planarity : 0.004 0.061 1330 Dihedral : 5.970 58.033 1163 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.38 % Allowed : 18.46 % Favored : 78.15 % 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: -2.16 (0.26), residues: 1047 helix: 0.80 (0.31), residues: 319 sheet: -2.39 (0.29), residues: 273 loop : -2.43 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 82 HIS 0.007 0.001 HIS B 225 PHE 0.023 0.002 PHE B 235 TYR 0.013 0.002 TYR E 190 ARG 0.003 0.001 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.790 Fit side-chains REVERT: A 297 GLU cc_start: 0.7283 (tp30) cc_final: 0.7050 (tp30) REVERT: A 333 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 10 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5951 (tp30) REVERT: B 17 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 51 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8312 (mt) REVERT: B 222 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: E 246 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6924 (mm-30) REVERT: R 117 ARG cc_start: 0.8106 (mtm110) cc_final: 0.7633 (mtm110) REVERT: R 169 TRP cc_start: 0.7424 (p90) cc_final: 0.7081 (p90) REVERT: R 217 PHE cc_start: 0.6352 (OUTLIER) cc_final: 0.4560 (t80) outliers start: 22 outliers final: 10 residues processed: 103 average time/residue: 0.2268 time to fit residues: 30.9378 Evaluate side-chains 96 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 217 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.0470 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7647 Z= 0.185 Angle : 0.555 8.951 10443 Z= 0.293 Chirality : 0.041 0.135 1255 Planarity : 0.004 0.056 1330 Dihedral : 5.475 54.772 1163 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.23 % Allowed : 18.77 % Favored : 78.00 % 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: -1.87 (0.26), residues: 1047 helix: 1.07 (0.32), residues: 314 sheet: -2.19 (0.30), residues: 266 loop : -2.28 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.012 0.001 PHE B 235 TYR 0.015 0.001 TYR R 184 ARG 0.003 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.822 Fit side-chains REVERT: A 297 GLU cc_start: 0.7270 (tp30) cc_final: 0.7012 (tp30) REVERT: A 333 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7632 (tm-30) REVERT: B 17 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8091 (tm-30) REVERT: B 51 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8181 (mt) REVERT: E 246 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6907 (mm-30) REVERT: R 117 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7577 (mtm110) REVERT: R 169 TRP cc_start: 0.7429 (p90) cc_final: 0.7072 (p90) outliers start: 21 outliers final: 13 residues processed: 102 average time/residue: 0.2163 time to fit residues: 29.6071 Evaluate side-chains 96 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 56 optimal weight: 0.0970 chunk 101 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7647 Z= 0.151 Angle : 0.536 8.299 10443 Z= 0.279 Chirality : 0.041 0.131 1255 Planarity : 0.004 0.059 1330 Dihedral : 5.151 53.870 1163 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.92 % Allowed : 19.38 % Favored : 77.69 % 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: -1.57 (0.27), residues: 1047 helix: 1.34 (0.32), residues: 315 sheet: -1.93 (0.30), residues: 275 loop : -2.18 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.008 0.001 PHE A 196 TYR 0.017 0.001 TYR R 184 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.808 Fit side-chains REVERT: B 17 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8108 (tm-30) REVERT: B 51 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8204 (mt) REVERT: B 300 LEU cc_start: 0.7779 (tt) cc_final: 0.7547 (mm) REVERT: E 246 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6653 (mm-30) REVERT: R 117 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7586 (mtm110) REVERT: R 169 TRP cc_start: 0.7452 (p90) cc_final: 0.7063 (p90) outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 0.2220 time to fit residues: 31.4957 Evaluate side-chains 98 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 30.0000 chunk 96 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7647 Z= 0.203 Angle : 0.571 8.590 10443 Z= 0.297 Chirality : 0.042 0.131 1255 Planarity : 0.004 0.061 1330 Dihedral : 5.148 57.020 1163 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.92 % Allowed : 19.69 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.27), residues: 1047 helix: 1.41 (0.32), residues: 309 sheet: -1.98 (0.30), residues: 271 loop : -2.11 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 235 TYR 0.016 0.001 TYR R 184 ARG 0.010 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.766 Fit side-chains REVERT: A 21 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7679 (ttp-110) REVERT: B 17 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8112 (tm-30) REVERT: B 51 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8261 (mt) REVERT: E 246 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6686 (mm-30) REVERT: R 117 ARG cc_start: 0.7932 (mtm110) cc_final: 0.7474 (mtm110) REVERT: R 169 TRP cc_start: 0.7453 (p90) cc_final: 0.7088 (p90) outliers start: 19 outliers final: 14 residues processed: 100 average time/residue: 0.2225 time to fit residues: 29.6432 Evaluate side-chains 98 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.0000 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7647 Z= 0.168 Angle : 0.552 8.944 10443 Z= 0.287 Chirality : 0.041 0.130 1255 Planarity : 0.004 0.064 1330 Dihedral : 5.040 56.444 1163 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.77 % Allowed : 20.00 % Favored : 77.23 % 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: -1.40 (0.27), residues: 1047 helix: 1.51 (0.31), residues: 314 sheet: -1.85 (0.30), residues: 274 loop : -2.08 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.010 0.001 PHE B 234 TYR 0.016 0.001 TYR R 184 ARG 0.009 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.797 Fit side-chains REVERT: A 21 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7883 (tmm-80) REVERT: A 333 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7609 (tm-30) REVERT: B 17 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8110 (tm-30) REVERT: B 51 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8243 (mt) REVERT: B 300 LEU cc_start: 0.7695 (tt) cc_final: 0.7427 (mm) REVERT: E 34 MET cc_start: 0.7100 (tpp) cc_final: 0.6858 (tpp) REVERT: R 117 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7507 (mtm110) REVERT: R 169 TRP cc_start: 0.7443 (p90) cc_final: 0.7100 (p90) outliers start: 18 outliers final: 14 residues processed: 97 average time/residue: 0.2163 time to fit residues: 28.2234 Evaluate side-chains 95 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 0.0050 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7647 Z= 0.197 Angle : 0.569 9.612 10443 Z= 0.297 Chirality : 0.042 0.132 1255 Planarity : 0.004 0.065 1330 Dihedral : 5.086 56.031 1163 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.62 % Allowed : 20.77 % Favored : 76.62 % 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: -1.34 (0.27), residues: 1047 helix: 1.63 (0.31), residues: 313 sheet: -1.93 (0.30), residues: 271 loop : -2.01 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 235 TYR 0.016 0.001 TYR R 184 ARG 0.008 0.000 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.851 Fit side-chains REVERT: A 333 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 17 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 51 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8284 (mt) REVERT: B 300 LEU cc_start: 0.7771 (tt) cc_final: 0.7370 (mm) REVERT: E 34 MET cc_start: 0.7188 (tpp) cc_final: 0.6949 (tpp) REVERT: R 117 ARG cc_start: 0.7922 (mtm110) cc_final: 0.7465 (mtm110) REVERT: R 169 TRP cc_start: 0.7475 (p90) cc_final: 0.7131 (p90) outliers start: 17 outliers final: 14 residues processed: 100 average time/residue: 0.2108 time to fit residues: 28.1928 Evaluate side-chains 98 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.105003 restraints weight = 12240.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.103942 restraints weight = 7428.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105656 restraints weight = 6867.383| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7647 Z= 0.186 Angle : 0.562 9.715 10443 Z= 0.294 Chirality : 0.041 0.131 1255 Planarity : 0.004 0.065 1330 Dihedral : 5.041 55.792 1163 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.77 % Allowed : 20.62 % Favored : 76.62 % 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: -1.26 (0.27), residues: 1047 helix: 1.69 (0.31), residues: 314 sheet: -1.84 (0.31), residues: 268 loop : -1.99 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.011 0.001 PHE B 234 TYR 0.017 0.001 TYR R 184 ARG 0.013 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1629.12 seconds wall clock time: 30 minutes 26.59 seconds (1826.59 seconds total)