Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 17 14:39:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/08_2023/7ecw_31059.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/08_2023/7ecw_31059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/08_2023/7ecw_31059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/08_2023/7ecw_31059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/08_2023/7ecw_31059.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/08_2023/7ecw_31059.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 P 69 5.49 5 S 27 5.16 5 C 14163 2.51 5 N 4253 2.21 5 O 4577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 207": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "H GLU 321": "OE1" <-> "OE2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "J GLU 119": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 23089 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2251 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 266, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1200 Unresolved non-hydrogen angles: 1728 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 330 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 21, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 8, 'HIS:plan': 6, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 670 Chain: "B" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2364 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2264 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2534 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2569 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2556 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2552 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 122} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 995 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "M" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 928 Classifications: {'RNA': 44} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 11, 'rna3p_pyr': 13} Link IDs: {'rna2p': 18, 'rna3p': 25} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "O" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 12.09, per 1000 atoms: 0.52 Number of scatterers: 23089 At special positions: 0 Unit cell: (135.3, 134.2, 171.6, 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 27 16.00 P 69 15.00 O 4577 8.00 N 4253 7.00 C 14163 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.70 Conformation dependent library (CDL) restraints added in 3.6 seconds 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 38 sheets defined 32.1% alpha, 19.4% beta 10 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 7.75 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.559A pdb=" N LEU A 100 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.534A pdb=" N LYS A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 4.624A pdb=" N ASN A 132 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.793A pdb=" N GLU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.736A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 314 through 341 removed outlier: 3.806A pdb=" N ILE A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 385 through 399 removed outlier: 4.295A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 398 " --> pdb=" O TRP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 409 through 423 removed outlier: 4.080A pdb=" N GLN A 413 " --> pdb=" O PRO A 409 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'B' and resid 33 through 53 removed outlier: 4.000A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.569A pdb=" N ILE B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 178 through 181 removed outlier: 4.057A pdb=" N LEU B 181 " --> pdb=" O ARG B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 207 through 212 removed outlier: 3.847A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 207 through 212' Processing helix chain 'B' and resid 291 through 295 removed outlier: 4.009A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.757A pdb=" N ASP B 300 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 301' Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.873A pdb=" N GLN C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 129 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.611A pdb=" N ALA C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 205 removed outlier: 3.787A pdb=" N GLY C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.776A pdb=" N ILE C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 Processing helix chain 'C' and resid 319 through 329 removed outlier: 3.768A pdb=" N TYR C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.837A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.929A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.649A pdb=" N ARG D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 205 removed outlier: 3.742A pdb=" N LEU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.821A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 322 through 332 removed outlier: 4.343A pdb=" N VAL D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 327 " --> pdb=" O GLN D 323 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 36 removed outlier: 3.875A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 removed outlier: 4.169A pdb=" N ILE E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.977A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.971A pdb=" N ARG E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 203 removed outlier: 3.937A pdb=" N ALA E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.693A pdb=" N ILE E 260 " --> pdb=" O HIS E 256 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 312 removed outlier: 3.550A pdb=" N LEU E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASP E 309 " --> pdb=" O TYR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.792A pdb=" N HIS E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 326 " --> pdb=" O GLN E 322 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.732A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 70 removed outlier: 3.562A pdb=" N ASP F 68 " --> pdb=" O PRO F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 4.250A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 191 through 205 removed outlier: 3.843A pdb=" N LEU F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.583A pdb=" N ILE F 260 " --> pdb=" O HIS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 313 Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.868A pdb=" N HIS F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY F 333 " --> pdb=" O ASN F 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 removed outlier: 4.042A pdb=" N ASP G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN G 72 " --> pdb=" O ASP G 68 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.850A pdb=" N ARG G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.705A pdb=" N ASN G 141 " --> pdb=" O ARG G 137 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 142 " --> pdb=" O TYR G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 205 removed outlier: 3.893A pdb=" N LEU G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 205 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 263 removed outlier: 3.502A pdb=" N ALA G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 removed outlier: 3.508A pdb=" N ASP G 309 " --> pdb=" O TYR G 305 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G 313 " --> pdb=" O ASP G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 removed outlier: 3.845A pdb=" N HIS G 324 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL G 326 " --> pdb=" O GLN G 322 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 327 " --> pdb=" O GLN G 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.607A pdb=" N SER H 36 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 72 removed outlier: 3.748A pdb=" N GLN H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 129 removed outlier: 3.591A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 139 Processing helix chain 'H' and resid 139 through 144 Processing helix chain 'H' and resid 191 through 204 removed outlier: 3.936A pdb=" N LEU H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.722A pdb=" N ILE H 260 " --> pdb=" O HIS H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 313 removed outlier: 3.722A pdb=" N LEU H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 333 removed outlier: 3.991A pdb=" N TYR H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL H 326 " --> pdb=" O GLN H 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE H 327 " --> pdb=" O GLN H 323 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY H 333 " --> pdb=" O ASN H 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 12 Processing helix chain 'I' and resid 21 through 30 Processing helix chain 'I' and resid 42 through 56 removed outlier: 3.969A pdb=" N ILE I 46 " --> pdb=" O SER I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 75 Processing helix chain 'I' and resid 109 through 121 Processing helix chain 'J' and resid 3 through 12 Processing helix chain 'J' and resid 21 through 30 Processing helix chain 'J' and resid 42 through 56 removed outlier: 3.969A pdb=" N ILE J 46 " --> pdb=" O SER J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 75 Processing helix chain 'J' and resid 109 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.539A pdb=" N PHE B 184 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE B 61 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N SER B 188 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 14.042A pdb=" N VAL B 59 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 59 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY B 112 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 61 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU B 110 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N CYS B 63 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER B 108 " --> pdb=" O CYS B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 21 removed outlier: 5.323A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER B 108 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N CYS B 63 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU B 110 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 61 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY B 112 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 59 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 14.042A pdb=" N VAL B 59 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N SER B 188 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE B 61 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 184 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 14 removed outlier: 3.695A pdb=" N LEU C 12 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.688A pdb=" N ALA C 157 " --> pdb=" O ARG C 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 20 removed outlier: 4.593A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 44 through 47 removed outlier: 4.564A pdb=" N ARG C 45 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 81 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.609A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.603A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA D 157 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 172 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.603A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D 28 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 44 through 49 removed outlier: 4.744A pdb=" N ALA D 82 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 229 through 230 removed outlier: 4.753A pdb=" N THR D 245 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 266 through 268 removed outlier: 3.800A pdb=" N ASP D 268 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.526A pdb=" N LEU E 12 " --> pdb=" O PHE E 336 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.957A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG E 172 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.547A pdb=" N ARG E 94 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 24 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 49 removed outlier: 7.737A pdb=" N THR E 78 " --> pdb=" O SER E 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AC5, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.689A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU F 12 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.844A pdb=" N VAL F 99 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA F 157 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL F 158 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP F 177 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE F 162 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.501A pdb=" N ALA F 23 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 44 through 51 removed outlier: 4.110A pdb=" N PHE I 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR F 78 " --> pdb=" O PHE I 104 " (cutoff:3.500A) removed outlier: 11.528A pdb=" N CYS I 106 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 14.996A pdb=" N ASP F 80 " --> pdb=" O CYS I 106 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR I 102 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER I 96 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE I 104 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LYS I 94 " --> pdb=" O PHE I 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AD1, first strand: chain 'G' and resid 108 through 109 Processing sheet with id=AD2, first strand: chain 'G' and resid 18 through 20 removed outlier: 4.167A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.573A pdb=" N LEU G 24 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA G 253 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 45 through 51 removed outlier: 4.068A pdb=" N ASN G 75 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU G 76 " --> pdb=" O GLN G 241 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD6, first strand: chain 'G' and resid 287 through 288 removed outlier: 3.648A pdb=" N LYS G 293 " --> pdb=" O VAL G 288 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.524A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY H 334 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.594A pdb=" N ASP H 19 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG H 98 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL H 158 " --> pdb=" O ASP H 177 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP H 177 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL H 160 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG H 175 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE H 162 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR H 173 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N HIS H 164 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.594A pdb=" N ASP H 19 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG H 98 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY H 28 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 45 through 51 removed outlier: 3.637A pdb=" N PHE J 104 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR H 78 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 11.500A pdb=" N CYS J 106 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 14.929A pdb=" N ASP H 80 " --> pdb=" O CYS J 106 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR J 102 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER J 96 " --> pdb=" O TYR J 102 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N PHE J 104 " --> pdb=" O LYS J 94 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS J 94 " --> pdb=" O PHE J 104 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 266 through 268 removed outlier: 3.637A pdb=" N ASP H 268 " --> pdb=" O ILE H 280 " (cutoff:3.500A) 849 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 8.43 Time building geometry restraints manager: 9.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4386 1.32 - 1.45: 6167 1.45 - 1.57: 12936 1.57 - 1.69: 136 1.69 - 1.81: 39 Bond restraints: 23664 Sorted by residual: bond pdb=" N ILE E 232 " pdb=" CA ILE E 232 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.64e+00 bond pdb=" N LEU A 268 " pdb=" CA LEU A 268 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.95e+00 bond pdb=" N GLN E 241 " pdb=" CA GLN E 241 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.91e+00 bond pdb=" N LEU E 233 " pdb=" CA LEU E 233 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" N LEU E 231 " pdb=" CA LEU E 231 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.56e+00 ... (remaining 23659 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.21: 626 105.21 - 112.57: 11789 112.57 - 119.92: 8648 119.92 - 127.28: 10883 127.28 - 134.64: 353 Bond angle restraints: 32299 Sorted by residual: angle pdb=" O3' DG N 33 " pdb=" C3' DG N 33 " pdb=" C2' DG N 33 " ideal model delta sigma weight residual 111.50 99.38 12.12 1.50e+00 4.44e-01 6.53e+01 angle pdb=" N GLY G 240 " pdb=" CA GLY G 240 " pdb=" C GLY G 240 " ideal model delta sigma weight residual 115.32 123.37 -8.05 1.38e+00 5.25e-01 3.40e+01 angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 109.34 97.85 11.49 2.08e+00 2.31e-01 3.05e+01 angle pdb=" N LEU G 233 " pdb=" CA LEU G 233 " pdb=" C LEU G 233 " ideal model delta sigma weight residual 111.36 117.29 -5.93 1.09e+00 8.42e-01 2.96e+01 angle pdb=" N VAL G 249 " pdb=" CA VAL G 249 " pdb=" C VAL G 249 " ideal model delta sigma weight residual 109.34 98.26 11.08 2.08e+00 2.31e-01 2.84e+01 ... (remaining 32294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.19: 12952 31.19 - 62.39: 614 62.39 - 93.58: 47 93.58 - 124.78: 0 124.78 - 155.97: 2 Dihedral angle restraints: 13615 sinusoidal: 5689 harmonic: 7926 Sorted by residual: dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 44.03 155.97 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 72.47 127.53 1 1.50e+01 4.44e-03 6.87e+01 dihedral pdb=" CA LEU B 12 " pdb=" C LEU B 12 " pdb=" N PRO B 13 " pdb=" CA PRO B 13 " ideal model delta harmonic sigma weight residual -180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 13612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2993 0.075 - 0.151: 423 0.151 - 0.226: 61 0.226 - 0.301: 4 0.301 - 0.377: 3 Chirality restraints: 3484 Sorted by residual: chirality pdb=" CA HIS B 305 " pdb=" N HIS B 305 " pdb=" C HIS B 305 " pdb=" CB HIS B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C3' DG N 33 " pdb=" C4' DG N 33 " pdb=" O3' DG N 33 " pdb=" C2' DG N 33 " both_signs ideal model delta sigma weight residual False -2.66 -3.01 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ALA G 319 " pdb=" N ALA G 319 " pdb=" C ALA G 319 " pdb=" CB ALA G 319 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 3481 not shown) Planarity restraints: 4078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 232 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ILE G 232 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE G 232 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU G 233 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 127 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C ASN C 127 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN C 127 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU C 128 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 228 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.30e+00 pdb=" N PRO A 229 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.038 5.00e-02 4.00e+02 ... (remaining 4075 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 111 2.54 - 3.13: 15611 3.13 - 3.72: 33173 3.72 - 4.31: 47071 4.31 - 4.90: 79839 Nonbonded interactions: 175805 Sorted by model distance: nonbonded pdb=" O ASN G 75 " pdb=" OD1 ASN G 75 " model vdw 1.950 3.040 nonbonded pdb=" OD1 ASP H 111 " pdb=" N ALA H 112 " model vdw 2.174 2.520 nonbonded pdb=" O LEU B 139 " pdb=" O2 U M 2 " model vdw 2.202 3.040 nonbonded pdb=" CG1 VAL A 199 " pdb=" NH1 ARG A 258 " model vdw 2.218 3.540 nonbonded pdb=" O VAL I 36 " pdb=" OD1 ASP I 37 " model vdw 2.270 3.040 ... (remaining 175800 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 6 through 230 or (resid 231 and (name N or name CA or name \ C or name O or name CB )) or resid 244 through 272 or (resid 273 through 275 an \ d (name N or name CA or name C or name O or name CB )) or resid 276 through 337 \ or (resid 338 and (name N or name CA or name C or name O )))) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 231 or re \ sid 244 through 323 or (resid 324 and (name N or name CA or name C or name O or \ name CB )) or resid 325 through 337 or (resid 338 and (name N or name CA or name \ C or name O )))) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O )))) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O )))) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O )))) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 338)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 124)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.050 Extract box with map and model: 5.330 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 62.790 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.130 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 0.080 23664 Z= 0.440 Angle : 0.887 12.122 32299 Z= 0.511 Chirality : 0.056 0.377 3484 Planarity : 0.006 0.068 4078 Dihedral : 16.808 155.975 8683 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.06 % Favored : 93.81 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.04 % 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: -3.73 (0.12), residues: 2906 helix: -3.20 (0.11), residues: 880 sheet: -0.28 (0.25), residues: 445 loop : -2.77 (0.12), residues: 1581 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 314 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 332 average time/residue: 0.4787 time to fit residues: 224.1906 Evaluate side-chains 240 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 230 time to evaluate : 2.499 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2630 time to fit residues: 7.9992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 0.0470 chunk 224 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 chunk 76 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 232 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 268 optimal weight: 7.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 188 HIS B 19 ASN B 45 GLN B 82 ASN B 269 ASN B 293 HIS B 305 HIS C 83 ASN C 140 HIS C 163 ASN C 167 GLN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN D 291 GLN ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN E 163 ASN E 229 GLN E 291 GLN E 310 ASN F 110 ASN F 129 GLN F 163 ASN F 241 GLN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN G 310 ASN H 77 GLN H 223 GLN H 241 GLN I 14 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 23664 Z= 0.148 Angle : 0.522 9.057 32299 Z= 0.282 Chirality : 0.040 0.223 3484 Planarity : 0.004 0.055 4078 Dihedral : 12.806 155.514 3954 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer Outliers : 2.29 % 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: -2.21 (0.14), residues: 2906 helix: -1.14 (0.16), residues: 884 sheet: 0.30 (0.24), residues: 455 loop : -2.28 (0.14), residues: 1567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 247 time to evaluate : 2.653 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 27 residues processed: 283 average time/residue: 0.4333 time to fit residues: 178.7133 Evaluate side-chains 246 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 219 time to evaluate : 2.596 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2172 time to fit residues: 13.7076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 chunk 183 optimal weight: 0.5980 chunk 74 optimal weight: 30.0000 chunk 269 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 267 optimal weight: 10.0000 chunk 91 optimal weight: 0.0040 chunk 216 optimal weight: 0.2980 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 68 HIS B 114 HIS ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN D 322 GLN E 167 GLN F 297 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 23664 Z= 0.211 Angle : 0.553 9.872 32299 Z= 0.293 Chirality : 0.041 0.222 3484 Planarity : 0.004 0.049 4078 Dihedral : 12.723 154.571 3954 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.25 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 2906 helix: -0.20 (0.17), residues: 890 sheet: 0.69 (0.25), residues: 445 loop : -2.08 (0.14), residues: 1571 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 225 time to evaluate : 2.390 Fit side-chains outliers start: 44 outliers final: 22 residues processed: 258 average time/residue: 0.4324 time to fit residues: 163.4336 Evaluate side-chains 237 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 215 time to evaluate : 2.526 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2202 time to fit residues: 12.2591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 139 optimal weight: 0.1980 chunk 29 optimal weight: 30.0000 chunk 128 optimal weight: 0.0980 chunk 180 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 256 optimal weight: 0.0050 chunk 77 optimal weight: 10.0000 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 151 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 229 GLN F 110 ASN G 77 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23664 Z= 0.178 Angle : 0.515 9.865 32299 Z= 0.274 Chirality : 0.040 0.219 3484 Planarity : 0.004 0.048 4078 Dihedral : 12.497 153.778 3954 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.70 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 2906 helix: 0.34 (0.18), residues: 888 sheet: 0.78 (0.26), residues: 434 loop : -1.96 (0.14), residues: 1584 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 226 time to evaluate : 2.455 Fit side-chains outliers start: 31 outliers final: 13 residues processed: 249 average time/residue: 0.4483 time to fit residues: 163.0410 Evaluate side-chains 224 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2404 time to fit residues: 8.8415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 0 optimal weight: 60.0000 chunk 146 optimal weight: 4.9990 chunk 256 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN G 77 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 23664 Z= 0.265 Angle : 0.578 9.810 32299 Z= 0.306 Chirality : 0.042 0.223 3484 Planarity : 0.004 0.051 4078 Dihedral : 12.565 153.599 3954 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 2906 helix: 0.46 (0.18), residues: 889 sheet: 0.87 (0.25), residues: 441 loop : -1.96 (0.14), residues: 1576 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 211 time to evaluate : 2.613 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 236 average time/residue: 0.4472 time to fit residues: 152.8444 Evaluate side-chains 215 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 2.302 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1965 time to fit residues: 9.9151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 10.0000 chunk 257 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 286 optimal weight: 0.9980 chunk 237 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 HIS ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 23664 Z= 0.179 Angle : 0.521 13.220 32299 Z= 0.276 Chirality : 0.040 0.217 3484 Planarity : 0.004 0.050 4078 Dihedral : 12.354 152.756 3954 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 1.00 % 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: -0.82 (0.16), residues: 2906 helix: 0.71 (0.18), residues: 896 sheet: 0.88 (0.25), residues: 464 loop : -1.85 (0.15), residues: 1546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 2.478 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 230 average time/residue: 0.4481 time to fit residues: 149.8761 Evaluate side-chains 214 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 205 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2068 time to fit residues: 6.8015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 6.9990 chunk 32 optimal weight: 40.0000 chunk 163 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 285 optimal weight: 0.0170 chunk 178 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN G 77 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 23664 Z= 0.206 Angle : 0.541 12.825 32299 Z= 0.286 Chirality : 0.041 0.221 3484 Planarity : 0.004 0.044 4078 Dihedral : 12.297 152.843 3954 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.16), residues: 2906 helix: 0.80 (0.18), residues: 896 sheet: 0.90 (0.25), residues: 446 loop : -1.80 (0.15), residues: 1564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 2.420 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 208 average time/residue: 0.4616 time to fit residues: 138.4335 Evaluate side-chains 205 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 2.381 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2356 time to fit residues: 8.1977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 23664 Z= 0.196 Angle : 0.531 12.302 32299 Z= 0.281 Chirality : 0.040 0.220 3484 Planarity : 0.004 0.044 4078 Dihedral : 12.195 152.422 3954 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.38 % 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: -0.65 (0.16), residues: 2906 helix: 0.90 (0.18), residues: 897 sheet: 0.95 (0.25), residues: 451 loop : -1.75 (0.15), residues: 1558 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 205 time to evaluate : 2.587 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 211 average time/residue: 0.4755 time to fit residues: 144.6531 Evaluate side-chains 203 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 200 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2194 time to fit residues: 4.5338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 265 optimal weight: 3.9990 chunk 160 optimal weight: 0.0670 chunk 115 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 251 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 HIS E 167 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 23664 Z= 0.194 Angle : 0.533 11.974 32299 Z= 0.282 Chirality : 0.040 0.221 3484 Planarity : 0.004 0.045 4078 Dihedral : 12.152 152.162 3954 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2906 helix: 0.95 (0.18), residues: 898 sheet: 0.97 (0.25), residues: 451 loop : -1.72 (0.15), residues: 1557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 2.327 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 202 average time/residue: 0.4555 time to fit residues: 132.6052 Evaluate side-chains 197 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 2.541 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2036 time to fit residues: 5.6417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 3.9990 chunk 281 optimal weight: 0.0170 chunk 171 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 23664 Z= 0.175 Angle : 0.520 11.687 32299 Z= 0.274 Chirality : 0.040 0.221 3484 Planarity : 0.004 0.044 4078 Dihedral : 12.083 151.544 3954 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2906 helix: 1.03 (0.18), residues: 897 sheet: 1.03 (0.25), residues: 451 loop : -1.68 (0.15), residues: 1558 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 2.425 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 193 average time/residue: 0.4531 time to fit residues: 127.8060 Evaluate side-chains 196 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2071 time to fit residues: 4.5615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 2.9990 chunk 250 optimal weight: 0.0980 chunk 71 optimal weight: 0.2980 chunk 216 optimal weight: 5.9990 chunk 34 optimal weight: 0.0770 chunk 65 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 241 optimal weight: 2.9990 chunk 29 optimal weight: 40.0000 chunk 43 optimal weight: 6.9990 overall best weight: 0.4340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 HIS C 140 HIS ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.182930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.144019 restraints weight = 27509.486| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.98 r_work: 0.3162 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 23664 Z= 0.117 Angle : 0.472 11.267 32299 Z= 0.249 Chirality : 0.038 0.217 3484 Planarity : 0.003 0.044 4078 Dihedral : 11.873 151.238 3954 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2906 helix: 1.33 (0.19), residues: 888 sheet: 1.18 (0.26), residues: 433 loop : -1.55 (0.15), residues: 1585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4707.84 seconds wall clock time: 85 minutes 57.94 seconds (5157.94 seconds total)