Starting phenix.real_space_refine on Wed Sep 25 01:33:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/09_2024/7nzm_12665.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/09_2024/7nzm_12665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/09_2024/7nzm_12665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/09_2024/7nzm_12665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/09_2024/7nzm_12665.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/09_2024/7nzm_12665.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 Mn 1 7.51 5 P 4 5.49 5 S 53 5.16 5 C 5776 2.51 5 N 1538 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9109 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1392 Classifications: {'peptide': 178} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 173} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2312 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 279} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2884 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2024 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 437 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "F" 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.68, per 1000 atoms: 0.62 Number of scatterers: 9109 At special positions: 0 Unit cell: (95.192, 110.84, 112.144, 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) Mn 1 24.99 S 53 16.00 P 4 15.00 O 1737 8.00 N 1538 7.00 C 5776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN D 18 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 995.5 milliseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 13 sheets defined 46.8% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'E' and resid 55 through 66 removed outlier: 4.279A pdb=" N ILE E 58 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE E 62 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG E 63 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY E 65 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 118 removed outlier: 3.824A pdb=" N LYS E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 117 " --> pdb=" O HIS E 113 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 133 through 142 Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.789A pdb=" N TYR E 149 " --> pdb=" O GLY E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 157 No H-bonds generated for 'chain 'E' and resid 156 through 157' Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 168 through 181 removed outlier: 3.529A pdb=" N VAL E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE E 179 " --> pdb=" O LEU E 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 3.767A pdb=" N ILE B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 42 through 49 removed outlier: 4.549A pdb=" N PHE B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 80 removed outlier: 3.788A pdb=" N GLU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.545A pdb=" N THR B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 199 through 207 removed outlier: 3.595A pdb=" N LEU B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 239 removed outlier: 3.525A pdb=" N LYS B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.645A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.568A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.614A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.594A pdb=" N GLY A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 207 through 217 removed outlier: 4.074A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.661A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 Proline residue: A 258 - end of helix removed outlier: 4.486A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.564A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.928A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.533A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.880A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.078A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 18 removed outlier: 3.833A pdb=" N ASN D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 31 removed outlier: 3.645A pdb=" N ARG D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 56 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 139 through 159 removed outlier: 4.237A pdb=" N TYR D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP D 149 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.881A pdb=" N SER D 182 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 234 through 240 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'C' and resid 582 through 604 removed outlier: 3.564A pdb=" N ARG C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 588 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 591 " --> pdb=" O ARG C 587 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR C 597 " --> pdb=" O ALA C 593 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU C 602 " --> pdb=" O GLN C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 608 through 618 removed outlier: 3.743A pdb=" N ARG C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TRP C 616 " --> pdb=" O ARG C 612 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 617 " --> pdb=" O ALA C 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 18 through 27 removed outlier: 6.708A pdb=" N TYR E 32 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE E 26 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA E 31 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE E 82 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR E 81 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL E 75 " --> pdb=" O TYR E 81 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP E 83 " --> pdb=" O ILE E 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.876A pdb=" N LEU B 59 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 285 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N THR C 563 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE B 293 " --> pdb=" O THR C 563 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N HIS C 565 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE B 295 " --> pdb=" O HIS C 565 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209 removed outlier: 6.813A pdb=" N ASP B 208 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.508A pdb=" N VAL B 264 " --> pdb=" O ILE B 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.656A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.453A pdb=" N VAL A 43 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG D 79 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU D 39 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL D 40 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR D 10 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 255 " --> pdb=" O ALA D 5 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU D 256 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA D 231 " --> pdb=" O GLU D 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.650A pdb=" N ASN A 162 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 176 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.236A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.501A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 240 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 248 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 90 through 96 removed outlier: 7.459A pdb=" N LYS D 117 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR D 94 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL D 115 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA D 114 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE D 118 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE D 128 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N MET D 164 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALA D 129 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N MET D 166 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL D 131 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP D 168 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU D 133 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG D 213 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL D 216 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN D 193 " --> pdb=" O VAL D 216 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 978 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: 2.50 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2587 1.33 - 1.45: 1632 1.45 - 1.57: 4997 1.57 - 1.70: 9 1.70 - 1.82: 80 Bond restraints: 9305 Sorted by residual: bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.11e+01 bond pdb=" C5 ATP A 401 " pdb=" C6 ATP A 401 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.61e+01 bond pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.53e+01 bond pdb=" C5 ATP A 401 " pdb=" N7 ATP A 401 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.51e+01 bond pdb=" C8 ATP A 401 " pdb=" N7 ATP A 401 " ideal model delta sigma weight residual 1.310 1.352 -0.042 1.00e-02 1.00e+04 1.80e+01 ... (remaining 9300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 12532 4.30 - 8.59: 94 8.59 - 12.89: 6 12.89 - 17.18: 1 17.18 - 21.48: 2 Bond angle restraints: 12635 Sorted by residual: angle pdb=" PA ATP A 401 " pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " ideal model delta sigma weight residual 136.83 115.35 21.48 1.00e+00 1.00e+00 4.61e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 118.69 21.18 1.00e+00 1.00e+00 4.49e+02 angle pdb=" C5 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N3 ATP A 401 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" N3 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 127.04 134.93 -7.89 1.15e+00 7.59e-01 4.72e+01 angle pdb=" C ARG B 96 " pdb=" N GLY B 97 " pdb=" CA GLY B 97 " ideal model delta sigma weight residual 121.67 114.60 7.07 1.43e+00 4.89e-01 2.45e+01 ... (remaining 12630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5118 18.00 - 36.00: 402 36.00 - 54.00: 79 54.00 - 72.00: 19 72.00 - 90.00: 11 Dihedral angle restraints: 5629 sinusoidal: 2247 harmonic: 3382 Sorted by residual: dihedral pdb=" CA LEU D 133 " pdb=" C LEU D 133 " pdb=" N HIS D 134 " pdb=" CA HIS D 134 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CB CYS E 69 " pdb=" SG CYS E 69 " pdb=" SG CYS E 97 " pdb=" CB CYS E 97 " ideal model delta sinusoidal sigma weight residual 93.00 55.62 37.38 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA VAL A 43 " pdb=" C VAL A 43 " pdb=" N MET A 44 " pdb=" CA MET A 44 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1078 0.065 - 0.129: 295 0.129 - 0.194: 36 0.194 - 0.259: 4 0.259 - 0.323: 2 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA ARG B 96 " pdb=" N ARG B 96 " pdb=" C ARG B 96 " pdb=" CB ARG B 96 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA CYS A 257 " pdb=" N CYS A 257 " pdb=" C CYS A 257 " pdb=" CB CYS A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA GLU E 16 " pdb=" N GLU E 16 " pdb=" C GLU E 16 " pdb=" CB GLU E 16 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1412 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 90 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO E 91 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO E 91 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO E 91 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 111 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO A 112 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 76 " 0.024 2.00e-02 2.50e+03 1.86e-02 6.91e+00 pdb=" CG TYR D 76 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 76 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR D 76 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 76 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 76 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 76 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 76 " 0.001 2.00e-02 2.50e+03 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 21 2.40 - 3.02: 5360 3.02 - 3.65: 12874 3.65 - 4.27: 19327 4.27 - 4.90: 32191 Nonbonded interactions: 69773 Sorted by model distance: nonbonded pdb=" OD2 ASP B 92 " pdb="MN MN B 401 " model vdw 1.774 2.320 nonbonded pdb=" ND1 HIS B 248 " pdb="MN MN B 401 " model vdw 1.926 2.400 nonbonded pdb=" NE2 HIS B 173 " pdb="MN MN B 401 " model vdw 1.993 2.400 nonbonded pdb=" CE1 HIS B 248 " pdb="MN MN B 401 " model vdw 1.999 2.540 nonbonded pdb=" O LEU B 38 " pdb=" OG SER B 42 " model vdw 2.110 3.040 ... (remaining 69768 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.470 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 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 : 0.007 0.071 9305 Z= 0.440 Angle : 1.122 21.476 12635 Z= 0.685 Chirality : 0.058 0.323 1415 Planarity : 0.006 0.114 1627 Dihedral : 14.316 89.997 3445 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.56 (0.22), residues: 1144 helix: -1.35 (0.21), residues: 406 sheet: -0.40 (0.37), residues: 166 loop : -0.87 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 616 HIS 0.008 0.002 HIS B 248 PHE 0.023 0.003 PHE D 109 TYR 0.045 0.004 TYR D 76 ARG 0.015 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 603 LEU cc_start: 0.6489 (tp) cc_final: 0.6282 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2651 time to fit residues: 40.6179 Evaluate side-chains 67 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 ASN E 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5683 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9305 Z= 0.205 Angle : 0.716 12.217 12635 Z= 0.369 Chirality : 0.046 0.275 1415 Planarity : 0.004 0.081 1627 Dihedral : 7.097 89.867 1345 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.56 % Allowed : 6.65 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.31 (0.24), residues: 1144 helix: 0.00 (0.24), residues: 442 sheet: -0.25 (0.37), residues: 161 loop : -0.21 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 356 HIS 0.007 0.001 HIS B 173 PHE 0.019 0.001 PHE B 225 TYR 0.015 0.002 TYR D 32 ARG 0.006 0.001 ARG C 612 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 81 average time/residue: 0.2102 time to fit residues: 24.3089 Evaluate side-chains 61 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain D residue 133 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9305 Z= 0.194 Angle : 0.640 9.222 12635 Z= 0.331 Chirality : 0.044 0.183 1415 Planarity : 0.004 0.073 1627 Dihedral : 6.507 84.234 1345 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.35 % Allowed : 8.63 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.04 (0.24), residues: 1144 helix: 0.28 (0.24), residues: 452 sheet: 0.20 (0.41), residues: 140 loop : -0.08 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 356 HIS 0.005 0.001 HIS B 173 PHE 0.015 0.001 PHE B 225 TYR 0.018 0.001 TYR E 81 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 72 average time/residue: 0.1986 time to fit residues: 21.2111 Evaluate side-chains 59 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 77 optimal weight: 0.0970 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 overall best weight: 6.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS B 68 GLN B 239 HIS A 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9305 Z= 0.343 Angle : 0.735 11.124 12635 Z= 0.386 Chirality : 0.044 0.196 1415 Planarity : 0.005 0.069 1627 Dihedral : 6.900 86.921 1345 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.98 % Allowed : 10.50 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.02 (0.24), residues: 1144 helix: 0.01 (0.23), residues: 446 sheet: -0.05 (0.40), residues: 162 loop : 0.18 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 135 HIS 0.011 0.002 HIS A 161 PHE 0.019 0.002 PHE B 46 TYR 0.023 0.002 TYR D 32 ARG 0.007 0.001 ARG C 591 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 69 average time/residue: 0.2011 time to fit residues: 20.8517 Evaluate side-chains 57 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9305 Z= 0.183 Angle : 0.619 9.905 12635 Z= 0.315 Chirality : 0.042 0.155 1415 Planarity : 0.004 0.066 1627 Dihedral : 6.528 83.719 1345 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.83 % Allowed : 11.85 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.25 (0.25), residues: 1144 helix: 0.39 (0.24), residues: 461 sheet: -0.06 (0.42), residues: 147 loop : 0.23 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 79 HIS 0.007 0.001 HIS B 173 PHE 0.014 0.001 PHE B 225 TYR 0.020 0.001 TYR E 81 ARG 0.008 0.000 ARG C 591 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 1.076 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 60 average time/residue: 0.1853 time to fit residues: 17.3266 Evaluate side-chains 54 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 109 optimal weight: 0.0170 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9305 Z= 0.164 Angle : 0.615 10.678 12635 Z= 0.307 Chirality : 0.042 0.152 1415 Planarity : 0.004 0.062 1627 Dihedral : 6.341 87.438 1345 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.35 % Allowed : 12.68 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.41 (0.25), residues: 1144 helix: 0.57 (0.25), residues: 460 sheet: 0.05 (0.43), residues: 147 loop : 0.25 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 79 HIS 0.006 0.001 HIS B 173 PHE 0.012 0.001 PHE B 225 TYR 0.012 0.001 TYR E 81 ARG 0.006 0.000 ARG C 591 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 1.007 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 59 average time/residue: 0.1789 time to fit residues: 16.6318 Evaluate side-chains 54 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 68 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9305 Z= 0.151 Angle : 0.620 10.477 12635 Z= 0.304 Chirality : 0.042 0.152 1415 Planarity : 0.003 0.060 1627 Dihedral : 6.183 88.927 1345 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.04 % Allowed : 13.51 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.57 (0.25), residues: 1144 helix: 0.73 (0.25), residues: 455 sheet: 0.10 (0.43), residues: 147 loop : 0.33 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 79 HIS 0.005 0.001 HIS B 173 PHE 0.013 0.001 PHE B 225 TYR 0.011 0.001 TYR A 306 ARG 0.005 0.000 ARG C 591 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 1.159 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 59 average time/residue: 0.1964 time to fit residues: 17.5790 Evaluate side-chains 55 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN D 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9305 Z= 0.221 Angle : 0.652 10.750 12635 Z= 0.323 Chirality : 0.041 0.149 1415 Planarity : 0.004 0.080 1627 Dihedral : 6.303 83.810 1345 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.14 % Allowed : 14.35 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.66 (0.25), residues: 1144 helix: 0.82 (0.25), residues: 453 sheet: -0.07 (0.41), residues: 162 loop : 0.47 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 79 HIS 0.006 0.001 HIS B 173 PHE 0.012 0.001 PHE B 225 TYR 0.013 0.001 TYR D 32 ARG 0.006 0.000 ARG C 591 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7856 (pmm) cc_final: 0.7475 (pmm) outliers start: 11 outliers final: 7 residues processed: 58 average time/residue: 0.1749 time to fit residues: 16.1156 Evaluate side-chains 51 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 GLN A 296 ASN ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9305 Z= 0.299 Angle : 0.732 11.652 12635 Z= 0.366 Chirality : 0.043 0.173 1415 Planarity : 0.004 0.058 1627 Dihedral : 6.673 87.752 1345 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.04 % Allowed : 14.97 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.37 (0.25), residues: 1144 helix: 0.42 (0.24), residues: 457 sheet: -0.33 (0.40), residues: 162 loop : 0.51 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 149 HIS 0.008 0.002 HIS B 125 PHE 0.014 0.002 PHE B 225 TYR 0.019 0.002 TYR D 32 ARG 0.009 0.001 ARG C 591 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: D 16 MET cc_start: 0.6866 (ppp) cc_final: 0.6079 (ppp) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 0.1813 time to fit residues: 14.6834 Evaluate side-chains 50 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9305 Z= 0.267 Angle : 0.705 10.983 12635 Z= 0.352 Chirality : 0.042 0.152 1415 Planarity : 0.004 0.057 1627 Dihedral : 6.646 88.138 1345 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.73 % Allowed : 14.97 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.36 (0.25), residues: 1144 helix: 0.45 (0.24), residues: 456 sheet: -0.37 (0.40), residues: 162 loop : 0.47 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 582 HIS 0.008 0.002 HIS B 173 PHE 0.013 0.002 PHE B 225 TYR 0.017 0.002 TYR D 175 ARG 0.008 0.001 ARG C 591 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 1.023 Fit side-chains REVERT: A 44 MET cc_start: 0.5618 (tpt) cc_final: 0.5304 (tpt) REVERT: A 47 MET cc_start: 0.7928 (pmm) cc_final: 0.7375 (pmm) REVERT: D 16 MET cc_start: 0.6759 (ppp) cc_final: 0.5923 (ppp) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.1815 time to fit residues: 13.7499 Evaluate side-chains 47 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0980 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.023504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.016685 restraints weight = 113781.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.017418 restraints weight = 68382.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.017957 restraints weight = 47536.775| |-----------------------------------------------------------------------------| r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9305 Z= 0.156 Angle : 0.699 12.150 12635 Z= 0.338 Chirality : 0.044 0.173 1415 Planarity : 0.003 0.056 1627 Dihedral : 6.216 82.788 1345 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.31 % Allowed : 15.49 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.58 (0.25), residues: 1144 helix: 0.82 (0.25), residues: 448 sheet: -0.19 (0.41), residues: 162 loop : 0.37 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 135 HIS 0.007 0.001 HIS B 173 PHE 0.014 0.001 PHE D 118 TYR 0.017 0.001 TYR A 306 ARG 0.007 0.000 ARG C 591 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1670.89 seconds wall clock time: 31 minutes 10.61 seconds (1870.61 seconds total)