Starting phenix.real_space_refine on Mon Nov 20 19:15:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d43_30568/11_2023/7d43_30568_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d43_30568/11_2023/7d43_30568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d43_30568/11_2023/7d43_30568.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d43_30568/11_2023/7d43_30568.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d43_30568/11_2023/7d43_30568_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d43_30568/11_2023/7d43_30568_updated.pdb" } resolution = 4.3 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= 0.002 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 2 5.49 5 S 142 5.16 5 C 19492 2.51 5 N 5519 2.21 5 O 5854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E ASP 279": "OD1" <-> "OD2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "E ASP 292": "OD1" <-> "OD2" Residue "F ASP 74": "OD1" <-> "OD2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 161": "OD1" <-> "OD2" Residue "F ARG 166": "NH1" <-> "NH2" Residue "F PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 299": "OE1" <-> "OE2" Residue "G TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 344": "NH1" <-> "NH2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 417": "NH1" <-> "NH2" Residue "G ARG 446": "NH1" <-> "NH2" Residue "G ASP 459": "OD1" <-> "OD2" Residue "G ASP 490": "OD1" <-> "OD2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 246": "OE1" <-> "OE2" Residue "H TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 344": "NH1" <-> "NH2" Residue "H ARG 417": "NH1" <-> "NH2" Residue "H ARG 446": "NH1" <-> "NH2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "I ARG 65": "NH1" <-> "NH2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 269": "NH1" <-> "NH2" Residue "I TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 299": "NH1" <-> "NH2" Residue "I PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 462": "OD1" <-> "OD2" Residue "J ARG 65": "NH1" <-> "NH2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 195": "NH1" <-> "NH2" Residue "J ARG 211": "NH1" <-> "NH2" Residue "J ARG 269": "NH1" <-> "NH2" Residue "J ARG 299": "NH1" <-> "NH2" Residue "J ARG 316": "NH1" <-> "NH2" Residue "J ASP 462": "OD1" <-> "OD2" Residue "J GLU 464": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 31009 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2262 Classifications: {'peptide': 293} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2249 Classifications: {'peptide': 291} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2476 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2538 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2438 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 10, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "F" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2430 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 10, 'TRANS': 332} Chain breaks: 4 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "I" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3358 Classifications: {'peptide': 427} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 408} Chain: "J" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3371 Classifications: {'peptide': 429} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 409} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1309 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 7, 'TRANS': 252} Unresolved chain links: 1 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 813 Unresolved non-hydrogen angles: 1032 Unresolved non-hydrogen dihedrals: 659 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 14, 'TYR:plan': 12, 'ASN:plan1': 13, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 27, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 450 Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 889 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 340 Chain: "M" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "P" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 2109 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 332} Link IDs: {'PTRANS': 22, 'TRANS': 398} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1128 Unresolved non-hydrogen angles: 1429 Unresolved non-hydrogen dihedrals: 906 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 18, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 9, 'PHE:plan': 11, 'GLU:plan': 27, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 536 Time building chain proxies: 16.59, per 1000 atoms: 0.54 Number of scatterers: 31009 At special positions: 0 Unit cell: (161.7, 174.93, 217.56, 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 142 16.00 P 2 15.00 O 5854 8.00 N 5519 7.00 C 19492 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: 13.57 Conformation dependent library (CDL) restraints added in 6.2 seconds 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8214 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 141 helices and 36 sheets defined 33.4% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.78 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 43 through 58 WARNING: missing atoms! Processing helix chain 'A' and resid 63 through 78 Processing helix chain 'A' and resid 88 through 118 removed outlier: 4.143A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.796A pdb=" N LEU A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 248 through 251 No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.522A pdb=" N GLU A 299 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 302 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 15 Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 43 through 59 WARNING: missing atoms! Processing helix chain 'B' and resid 63 through 76 Processing helix chain 'B' and resid 88 through 115 removed outlier: 4.681A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 161 through 171 removed outlier: 4.269A pdb=" N HIS B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 188 removed outlier: 4.727A pdb=" N GLY B 184 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET B 187 " --> pdb=" O GLY B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 293 through 304 removed outlier: 3.523A pdb=" N ILE B 301 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR B 304 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 77 through 97 removed outlier: 3.524A pdb=" N HIS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 158 removed outlier: 5.356A pdb=" N MET C 148 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU C 156 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 Processing helix chain 'C' and resid 202 through 209 Processing helix chain 'C' and resid 219 through 228 removed outlier: 4.804A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C 226 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER C 227 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 334 through 342 Processing helix chain 'C' and resid 346 through 348 No H-bonds generated for 'chain 'C' and resid 346 through 348' Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 31 through 48 Processing helix chain 'D' and resid 54 through 71 Processing helix chain 'D' and resid 76 through 97 Processing helix chain 'D' and resid 128 through 145 Processing helix chain 'D' and resid 147 through 157 removed outlier: 4.573A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 183 removed outlier: 4.438A pdb=" N ARG D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 210 Processing helix chain 'D' and resid 219 through 228 removed outlier: 4.908A pdb=" N PHE D 223 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET D 226 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER D 227 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 333 through 342 removed outlier: 4.198A pdb=" N TYR D 337 " --> pdb=" O PRO D 333 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 349 No H-bonds generated for 'chain 'D' and resid 347 through 349' Processing helix chain 'E' and resid 36 through 44 removed outlier: 4.132A pdb=" N LEU E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 69 removed outlier: 4.674A pdb=" N MET E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 95 Proline residue: E 95 - end of helix Processing helix chain 'E' and resid 114 through 121 Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 184 through 187 No H-bonds generated for 'chain 'E' and resid 184 through 187' Processing helix chain 'E' and resid 209 through 216 removed outlier: 3.640A pdb=" N ASP E 213 " --> pdb=" O LYS E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 235 removed outlier: 4.813A pdb=" N ILE E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 282 through 294 removed outlier: 3.914A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU E 293 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N SER E 294 " --> pdb=" O TRP E 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 45 Proline residue: F 39 - end of helix Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 86 through 96 Proline residue: F 95 - end of helix Processing helix chain 'F' and resid 114 through 123 removed outlier: 4.065A pdb=" N VAL F 118 " --> pdb=" O HIS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 228 through 236 Processing helix chain 'F' and resid 279 through 291 removed outlier: 4.308A pdb=" N ARG F 289 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 181 Processing helix chain 'G' and resid 192 through 194 No H-bonds generated for 'chain 'G' and resid 192 through 194' Processing helix chain 'G' and resid 205 through 215 Processing helix chain 'G' and resid 222 through 239 Processing helix chain 'G' and resid 248 through 266 removed outlier: 3.955A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 271 through 284 Processing helix chain 'G' and resid 293 through 311 Processing helix chain 'G' and resid 314 through 324 Processing helix chain 'G' and resid 340 through 351 Processing helix chain 'G' and resid 369 through 379 removed outlier: 4.273A pdb=" N ALA G 379 " --> pdb=" O SER G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 396 removed outlier: 5.674A pdb=" N SER G 392 " --> pdb=" O PRO G 389 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU G 395 " --> pdb=" O SER G 392 " (cutoff:3.500A) Proline residue: G 396 - end of helix Processing helix chain 'G' and resid 421 through 430 Processing helix chain 'G' and resid 440 through 442 No H-bonds generated for 'chain 'G' and resid 440 through 442' Processing helix chain 'G' and resid 460 through 463 Processing helix chain 'G' and resid 494 through 496 No H-bonds generated for 'chain 'G' and resid 494 through 496' Processing helix chain 'G' and resid 509 through 517 Proline residue: G 513 - end of helix Processing helix chain 'H' and resid 178 through 180 No H-bonds generated for 'chain 'H' and resid 178 through 180' Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 205 through 215 Processing helix chain 'H' and resid 222 through 239 Processing helix chain 'H' and resid 248 through 266 removed outlier: 4.808A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 271 through 285 Processing helix chain 'H' and resid 293 through 312 Processing helix chain 'H' and resid 315 through 325 removed outlier: 5.066A pdb=" N GLN H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 352 removed outlier: 4.511A pdb=" N GLU H 352 " --> pdb=" O GLU H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 379 removed outlier: 4.301A pdb=" N ALA H 379 " --> pdb=" O SER H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 394 removed outlier: 4.467A pdb=" N SER H 392 " --> pdb=" O PRO H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 421 through 429 Processing helix chain 'H' and resid 440 through 442 No H-bonds generated for 'chain 'H' and resid 440 through 442' Processing helix chain 'H' and resid 509 through 517 Proline residue: H 513 - end of helix removed outlier: 3.592A pdb=" N LEU H 516 " --> pdb=" O PRO H 513 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 61 No H-bonds generated for 'chain 'I' and resid 59 through 61' Processing helix chain 'I' and resid 75 through 85 Processing helix chain 'I' and resid 99 through 108 removed outlier: 5.137A pdb=" N LYS I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 140 Processing helix chain 'I' and resid 162 through 173 Processing helix chain 'I' and resid 228 through 233 removed outlier: 3.556A pdb=" N GLN I 232 " --> pdb=" O SER I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 261 Processing helix chain 'I' and resid 269 through 278 Processing helix chain 'I' and resid 303 through 313 Processing helix chain 'I' and resid 331 through 333 No H-bonds generated for 'chain 'I' and resid 331 through 333' Processing helix chain 'I' and resid 339 through 341 No H-bonds generated for 'chain 'I' and resid 339 through 341' Processing helix chain 'J' and resid 59 through 62 No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 76 through 85 Processing helix chain 'J' and resid 99 through 108 removed outlier: 3.764A pdb=" N LYS J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 112 No H-bonds generated for 'chain 'J' and resid 110 through 112' Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 162 through 174 Processing helix chain 'J' and resid 229 through 234 removed outlier: 3.848A pdb=" N SER J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 261 Processing helix chain 'J' and resid 269 through 278 Processing helix chain 'J' and resid 303 through 315 removed outlier: 4.382A pdb=" N ARG J 315 " --> pdb=" O ALA J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 341 No H-bonds generated for 'chain 'J' and resid 339 through 341' Processing helix chain 'K' and resid 77 through 79 No H-bonds generated for 'chain 'K' and resid 77 through 79' Processing helix chain 'K' and resid 91 through 117 Processing helix chain 'K' and resid 124 through 140 Processing helix chain 'K' and resid 146 through 157 Processing helix chain 'K' and resid 159 through 162 No H-bonds generated for 'chain 'K' and resid 159 through 162' Processing helix chain 'K' and resid 169 through 179 removed outlier: 4.429A pdb=" N ILE K 179 " --> pdb=" O LEU K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 222 Processing helix chain 'K' and resid 246 through 248 No H-bonds generated for 'chain 'K' and resid 246 through 248' Processing helix chain 'K' and resid 255 through 260 Processing helix chain 'L' and resid 91 through 117 Processing helix chain 'L' and resid 124 through 139 Processing helix chain 'L' and resid 146 through 154 Processing helix chain 'L' and resid 160 through 164 removed outlier: 3.633A pdb=" N SER L 164 " --> pdb=" O ILE L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 179 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'P' and resid 144 through 147 No H-bonds generated for 'chain 'P' and resid 144 through 147' Processing helix chain 'P' and resid 149 through 151 No H-bonds generated for 'chain 'P' and resid 149 through 151' Processing helix chain 'P' and resid 204 through 208 Processing helix chain 'P' and resid 234 through 236 No H-bonds generated for 'chain 'P' and resid 234 through 236' Processing sheet with id= A, first strand: chain 'A' and resid 149 through 153 removed outlier: 8.078A pdb=" N VAL A 152 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR A 176 " --> pdb=" O VAL A 152 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 193 through 196 Processing sheet with id= C, first strand: chain 'A' and resid 206 through 208 Processing sheet with id= D, first strand: chain 'B' and resid 124 through 127 removed outlier: 6.419A pdb=" N SER B 149 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N THR B 127 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TYR B 151 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 207 through 209 Processing sheet with id= F, first strand: chain 'C' and resid 164 through 167 removed outlier: 6.509A pdb=" N HIS C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR C 167 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE C 190 " --> pdb=" O THR C 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 231 through 234 removed outlier: 7.418A pdb=" N ILE C 234 " --> pdb=" O PRO C 264 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE C 266 " --> pdb=" O ILE C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 246 through 248 Processing sheet with id= I, first strand: chain 'D' and resid 164 through 166 removed outlier: 7.166A pdb=" N HIS D 188 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 246 through 248 Processing sheet with id= K, first strand: chain 'E' and resid 52 through 54 removed outlier: 6.928A pdb=" N VAL E 76 " --> pdb=" O VAL E 53 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 129 through 133 removed outlier: 6.865A pdb=" N TYR E 264 " --> pdb=" O MET E 130 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N MET E 132 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE E 266 " --> pdb=" O MET E 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.162A pdb=" N HIS E 196 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 379 through 381 removed outlier: 6.622A pdb=" N VAL E 396 " --> pdb=" O LEU E 380 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 52 through 54 removed outlier: 6.220A pdb=" N VAL F 76 " --> pdb=" O VAL F 53 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 158 through 161 Processing sheet with id= Q, first strand: chain 'G' and resid 334 through 336 removed outlier: 3.977A pdb=" N TYR G 336 " --> pdb=" O LEU G 402 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 360 through 362 Processing sheet with id= S, first strand: chain 'G' and resid 414 through 417 Processing sheet with id= T, first strand: chain 'G' and resid 435 through 437 removed outlier: 6.741A pdb=" N LEU G 499 " --> pdb=" O VAL G 436 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE G 507 " --> pdb=" O VAL G 500 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 400 through 402 removed outlier: 3.642A pdb=" N ASP H 362 " --> pdb=" O LEU H 386 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 414 through 417 Processing sheet with id= W, first strand: chain 'H' and resid 435 through 437 removed outlier: 6.170A pdb=" N LEU H 499 " --> pdb=" O VAL H 436 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 44 through 46 removed outlier: 6.912A pdb=" N GLU I 90 " --> pdb=" O ALA I 45 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'I' and resid 184 through 186 removed outlier: 6.542A pdb=" N HIS I 290 " --> pdb=" O PHE I 185 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'I' and resid 238 through 241 removed outlier: 5.341A pdb=" N ASP I 206 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL I 212 " --> pdb=" O ASP I 206 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 155 through 157 Processing sheet with id= AB, first strand: chain 'J' and resid 182 through 186 removed outlier: 6.762A pdb=" N HIS J 288 " --> pdb=" O MET J 183 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N PHE J 185 " --> pdb=" O HIS J 288 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N HIS J 290 " --> pdb=" O PHE J 185 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'J' and resid 239 through 241 removed outlier: 5.100A pdb=" N ASP J 206 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL J 212 " --> pdb=" O ASP J 206 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 373 through 375 Processing sheet with id= AE, first strand: chain 'K' and resid 18 through 21 removed outlier: 6.712A pdb=" N ASP K 83 " --> pdb=" O ILE K 73 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 30 through 35 Processing sheet with id= AG, first strand: chain 'L' and resid 19 through 21 Processing sheet with id= AH, first strand: chain 'L' and resid 41 through 43 removed outlier: 3.563A pdb=" N SER L 25 " --> pdb=" O TYR L 32 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER L 34 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL L 23 " --> pdb=" O SER L 34 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'P' and resid 279 through 281 Processing sheet with id= AJ, first strand: chain 'P' and resid 405 through 408 957 hydrogen bonds defined for protein. 2490 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: 9.41 Time building geometry restraints manager: 13.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10596 1.34 - 1.46: 5348 1.46 - 1.58: 15337 1.58 - 1.70: 9 1.70 - 1.82: 216 Bond restraints: 31506 Sorted by residual: bond pdb=" CA PRO P 94 " pdb=" C PRO P 94 " ideal model delta sigma weight residual 1.520 1.617 -0.098 1.42e-02 4.96e+03 4.76e+01 bond pdb=" CA SER P 95 " pdb=" C SER P 95 " ideal model delta sigma weight residual 1.521 1.574 -0.053 1.23e-02 6.61e+03 1.86e+01 bond pdb=" CA SER G 399 " pdb=" C SER G 399 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" CA HIS H 430 " pdb=" C HIS H 430 " ideal model delta sigma weight residual 1.524 1.461 0.064 1.66e-02 3.63e+03 1.47e+01 bond pdb=" CA LEU C 303 " pdb=" C LEU C 303 " ideal model delta sigma weight residual 1.524 1.447 0.076 2.25e-02 1.98e+03 1.15e+01 ... (remaining 31501 not shown) Histogram of bond angle deviations from ideal: 98.53 - 106.37: 853 106.37 - 114.21: 18777 114.21 - 122.05: 16951 122.05 - 129.90: 6166 129.90 - 137.74: 161 Bond angle restraints: 42908 Sorted by residual: angle pdb=" N PRO P 94 " pdb=" CA PRO P 94 " pdb=" C PRO P 94 " ideal model delta sigma weight residual 112.47 127.30 -14.83 2.06e+00 2.36e-01 5.18e+01 angle pdb=" N GLU P 439 " pdb=" CA GLU P 439 " pdb=" C GLU P 439 " ideal model delta sigma weight residual 110.50 120.43 -9.93 1.41e+00 5.03e-01 4.96e+01 angle pdb=" C GLN H 477 " pdb=" N ASN H 478 " pdb=" CA ASN H 478 " ideal model delta sigma weight residual 120.63 131.78 -11.15 1.61e+00 3.86e-01 4.80e+01 angle pdb=" C LEU A 238 " pdb=" N PHE A 239 " pdb=" CA PHE A 239 " ideal model delta sigma weight residual 122.37 116.19 6.18 9.30e-01 1.16e+00 4.42e+01 angle pdb=" O ASP P 93 " pdb=" C ASP P 93 " pdb=" N PRO P 94 " ideal model delta sigma weight residual 122.06 116.22 5.84 1.02e+00 9.61e-01 3.28e+01 ... (remaining 42903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 17141 17.94 - 35.88: 1626 35.88 - 53.82: 248 53.82 - 71.76: 32 71.76 - 89.70: 24 Dihedral angle restraints: 19071 sinusoidal: 6448 harmonic: 12623 Sorted by residual: dihedral pdb=" CA PRO P 94 " pdb=" C PRO P 94 " pdb=" N SER P 95 " pdb=" CA SER P 95 " ideal model delta harmonic sigma weight residual 180.00 110.55 69.45 0 5.00e+00 4.00e-02 1.93e+02 dihedral pdb=" CA TYR D 126 " pdb=" C TYR D 126 " pdb=" N ALA D 127 " pdb=" CA ALA D 127 " ideal model delta harmonic sigma weight residual 180.00 -145.02 -34.98 0 5.00e+00 4.00e-02 4.90e+01 dihedral pdb=" CA MET K 223 " pdb=" C MET K 223 " pdb=" N PRO K 224 " pdb=" CA PRO K 224 " ideal model delta harmonic sigma weight residual 180.00 146.78 33.22 0 5.00e+00 4.00e-02 4.41e+01 ... (remaining 19068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4419 0.075 - 0.150: 695 0.150 - 0.225: 19 0.225 - 0.300: 2 0.300 - 0.375: 1 Chirality restraints: 5136 Sorted by residual: chirality pdb=" CA PRO P 94 " pdb=" N PRO P 94 " pdb=" C PRO P 94 " pdb=" CB PRO P 94 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA TYR F 38 " pdb=" N TYR F 38 " pdb=" C TYR F 38 " pdb=" CB TYR F 38 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE G 312 " pdb=" CA ILE G 312 " pdb=" CG1 ILE G 312 " pdb=" CG2 ILE G 312 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 5133 not shown) Planarity restraints: 5626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL P 437 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C VAL P 437 " -0.056 2.00e-02 2.50e+03 pdb=" O VAL P 437 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY P 438 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP P 93 " 0.015 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C ASP P 93 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP P 93 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO P 94 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS I 192 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO I 193 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO I 193 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO I 193 " 0.038 5.00e-02 4.00e+02 ... (remaining 5623 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 651 2.59 - 3.17: 31626 3.17 - 3.75: 49058 3.75 - 4.32: 64922 4.32 - 4.90: 102590 Nonbonded interactions: 248847 Sorted by model distance: nonbonded pdb=" OG SER H 200 " pdb=" O ILE H 203 " model vdw 2.018 2.440 nonbonded pdb=" OH TYR E 38 " pdb=" OD2 ASP E 288 " model vdw 2.079 2.440 nonbonded pdb=" O TYR B 86 " pdb=" NZ LYS B 90 " model vdw 2.114 2.520 nonbonded pdb=" O THR F 56 " pdb=" NH1 ARG F 57 " model vdw 2.128 2.520 nonbonded pdb=" ND2 ASN H 455 " pdb=" O TYR H 489 " model vdw 2.141 2.520 ... (remaining 248842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 253 or resid 268 through 305)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 8 through 343 or (resid 344 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 345 through 351)) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = (chain 'E' and (resid 1 through 27 or resid 29 through 444)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 41 through 170 or (resid 171 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 172 through 467)) selection = (chain 'J' and resid 41 through 467) } 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: 1.650 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: 0.030 Extract box with map and model: 8.580 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 80.430 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 31506 Z= 0.434 Angle : 0.987 14.829 42908 Z= 0.583 Chirality : 0.051 0.375 5136 Planarity : 0.005 0.068 5626 Dihedral : 14.617 89.701 10857 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 28.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 18.29 % Favored : 81.62 % Rotamer: Outliers : 0.31 % Allowed : 9.65 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.12 % 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: -6.11 (0.09), residues: 4287 helix: -3.22 (0.10), residues: 1406 sheet: -4.28 (0.18), residues: 483 loop : -4.75 (0.09), residues: 2398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 281 time to evaluate : 3.711 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 290 average time/residue: 0.4540 time to fit residues: 210.2909 Evaluate side-chains 194 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 3.602 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2625 time to fit residues: 6.9918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 2.9990 chunk 325 optimal weight: 0.4980 chunk 180 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 336 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 389 optimal weight: 40.0000 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 116 HIS ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN C 138 ASN C 150 ASN C 261 HIS ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 280 ASN ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** E 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN F 218 ASN F 274 ASN G 213 GLN G 254 ASN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN G 411 ASN G 431 ASN ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 HIS H 479 HIS I 105 HIS I 200 ASN I 376 ASN J 177 ASN ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 GLN ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 263 ASN J 359 ASN J 384 HIS J 393 GLN J 440 ASN J 452 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31506 Z= 0.277 Angle : 0.737 10.633 42908 Z= 0.382 Chirality : 0.048 0.258 5136 Planarity : 0.005 0.070 5626 Dihedral : 6.845 85.862 4610 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 14.95 % Favored : 85.02 % Rotamer: Outliers : 0.14 % Allowed : 8.26 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -4.77 (0.11), residues: 4287 helix: -1.77 (0.12), residues: 1405 sheet: -3.94 (0.18), residues: 489 loop : -4.07 (0.10), residues: 2393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 272 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 276 average time/residue: 0.4394 time to fit residues: 198.4002 Evaluate side-chains 184 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 3.688 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2705 time to fit residues: 5.6758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 3.9990 chunk 120 optimal weight: 0.0040 chunk 324 optimal weight: 0.9990 chunk 265 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 390 optimal weight: 40.0000 chunk 421 optimal weight: 0.6980 chunk 347 optimal weight: 9.9990 chunk 387 optimal weight: 20.0000 chunk 133 optimal weight: 0.0030 chunk 313 optimal weight: 4.9990 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN C 188 HIS ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS E 203 HIS E 218 ASN F 32 ASN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 ASN G 478 ASN G 479 HIS H 281 ASN ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN I 333 GLN I 340 HIS ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 384 HIS J 440 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31506 Z= 0.191 Angle : 0.674 11.524 42908 Z= 0.345 Chirality : 0.046 0.332 5136 Planarity : 0.005 0.065 5626 Dihedral : 6.202 87.004 4610 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.54 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -3.80 (0.12), residues: 4287 helix: -0.80 (0.13), residues: 1403 sheet: -3.63 (0.19), residues: 483 loop : -3.52 (0.11), residues: 2401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.4008 time to fit residues: 208.5326 Evaluate side-chains 208 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 3.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 40.0000 chunk 293 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 186 optimal weight: 30.0000 chunk 262 optimal weight: 0.7980 chunk 391 optimal weight: 0.6980 chunk 414 optimal weight: 20.0000 chunk 204 optimal weight: 0.9980 chunk 371 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN H 194 GLN ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 384 HIS J 434 GLN J 440 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31506 Z= 0.206 Angle : 0.657 11.150 42908 Z= 0.334 Chirality : 0.046 0.223 5136 Planarity : 0.004 0.066 5626 Dihedral : 5.921 87.679 4610 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.54 % Favored : 89.43 % Rotamer: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -3.32 (0.12), residues: 4287 helix: -0.30 (0.14), residues: 1409 sheet: -3.35 (0.19), residues: 511 loop : -3.29 (0.12), residues: 2367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 3.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 297 average time/residue: 0.4128 time to fit residues: 206.9700 Evaluate side-chains 202 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 3.642 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3233 time to fit residues: 5.4245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 20.0000 chunk 235 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 308 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 353 optimal weight: 5.9990 chunk 286 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 372 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 HIS J 255 GLN J 384 HIS J 434 GLN J 440 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31506 Z= 0.201 Angle : 0.643 10.927 42908 Z= 0.325 Chirality : 0.046 0.254 5136 Planarity : 0.004 0.069 5626 Dihedral : 5.746 88.344 4610 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.01 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -3.05 (0.12), residues: 4287 helix: -0.11 (0.14), residues: 1413 sheet: -3.17 (0.20), residues: 512 loop : -3.12 (0.12), residues: 2362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.4000 time to fit residues: 191.8851 Evaluate side-chains 194 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 3.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 81 optimal weight: 0.4980 chunk 243 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 415 optimal weight: 30.0000 chunk 344 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 217 optimal weight: 0.4980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 263 ASN ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 384 HIS J 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 31506 Z= 0.255 Angle : 0.674 12.639 42908 Z= 0.340 Chirality : 0.046 0.216 5136 Planarity : 0.004 0.069 5626 Dihedral : 5.779 89.574 4610 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.27 % Favored : 88.71 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -2.97 (0.12), residues: 4287 helix: -0.06 (0.14), residues: 1412 sheet: -3.17 (0.20), residues: 517 loop : -3.04 (0.12), residues: 2358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 3.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.3875 time to fit residues: 180.1990 Evaluate side-chains 197 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 234 optimal weight: 0.9990 chunk 349 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 413 optimal weight: 30.0000 chunk 258 optimal weight: 0.1980 chunk 252 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN ** H 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 384 HIS J 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31506 Z= 0.206 Angle : 0.646 10.683 42908 Z= 0.326 Chirality : 0.046 0.263 5136 Planarity : 0.004 0.071 5626 Dihedral : 5.651 89.809 4610 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.10 % Favored : 89.88 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -2.76 (0.13), residues: 4287 helix: 0.08 (0.14), residues: 1407 sheet: -3.05 (0.21), residues: 503 loop : -2.88 (0.12), residues: 2377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.4122 time to fit residues: 190.9194 Evaluate side-chains 199 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 4.241 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 246 optimal weight: 0.3980 chunk 124 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 262 optimal weight: 0.6980 chunk 281 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 325 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 HIS ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 388 ASN J 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31506 Z= 0.206 Angle : 0.655 12.213 42908 Z= 0.328 Chirality : 0.046 0.240 5136 Planarity : 0.004 0.071 5626 Dihedral : 5.561 89.110 4610 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.98 % Favored : 89.99 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -2.65 (0.13), residues: 4287 helix: 0.15 (0.14), residues: 1414 sheet: -3.11 (0.20), residues: 503 loop : -2.78 (0.12), residues: 2370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 3.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.4119 time to fit residues: 187.6503 Evaluate side-chains 205 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 3.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 8.9990 chunk 396 optimal weight: 0.7980 chunk 361 optimal weight: 40.0000 chunk 385 optimal weight: 20.0000 chunk 231 optimal weight: 0.0770 chunk 167 optimal weight: 1.9990 chunk 302 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 348 optimal weight: 0.7980 chunk 364 optimal weight: 1.9990 chunk 383 optimal weight: 6.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN ** H 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31506 Z= 0.202 Angle : 0.652 15.054 42908 Z= 0.326 Chirality : 0.046 0.255 5136 Planarity : 0.004 0.071 5626 Dihedral : 5.503 88.727 4610 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.35 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -2.56 (0.13), residues: 4287 helix: 0.21 (0.14), residues: 1404 sheet: -2.92 (0.21), residues: 523 loop : -2.73 (0.12), residues: 2360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 3.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.3942 time to fit residues: 183.9273 Evaluate side-chains 202 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 3.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 0.8980 chunk 407 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 chunk 283 optimal weight: 3.9990 chunk 427 optimal weight: 50.0000 chunk 393 optimal weight: 2.9990 chunk 340 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 262 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31506 Z= 0.252 Angle : 0.676 11.683 42908 Z= 0.340 Chirality : 0.046 0.260 5136 Planarity : 0.004 0.071 5626 Dihedral : 5.579 87.311 4610 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.13 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -2.58 (0.13), residues: 4287 helix: 0.17 (0.14), residues: 1403 sheet: -2.81 (0.21), residues: 534 loop : -2.75 (0.12), residues: 2350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 4.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.4454 time to fit residues: 200.5296 Evaluate side-chains 193 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 3.469 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 0.1980 chunk 362 optimal weight: 50.0000 chunk 104 optimal weight: 6.9990 chunk 313 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 340 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 350 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.086821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.070155 restraints weight = 119261.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069787 restraints weight = 88212.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.070446 restraints weight = 75720.920| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 31506 Z= 0.317 Angle : 0.719 10.503 42908 Z= 0.364 Chirality : 0.048 0.282 5136 Planarity : 0.005 0.070 5626 Dihedral : 5.821 85.152 4610 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.69 % Favored : 87.29 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -2.75 (0.13), residues: 4287 helix: -0.01 (0.14), residues: 1408 sheet: -2.87 (0.21), residues: 528 loop : -2.85 (0.12), residues: 2351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5159.52 seconds wall clock time: 97 minutes 52.99 seconds (5872.99 seconds total)