Starting phenix.real_space_refine on Thu Mar 21 19:34:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d43_30568/03_2024/7d43_30568_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d43_30568/03_2024/7d43_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_30568/03_2024/7d43_30568.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d43_30568/03_2024/7d43_30568.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d43_30568/03_2024/7d43_30568_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d43_30568/03_2024/7d43_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 14.24, per 1000 atoms: 0.46 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: 12.85 Conformation dependent library (CDL) restraints added in 6.4 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: 5.71 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: 8.48 Time building geometry restraints manager: 13.78 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: 1.250 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: 0.020 Extract box with map and model: 7.240 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 77.310 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.350 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP H 350 HIS 0.013 0.002 HIS B 128 PHE 0.022 0.002 PHE D 278 TYR 0.024 0.002 TYR H 214 ARG 0.009 0.001 ARG H 301 *********************** 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 : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7557 (mmp) cc_final: 0.7161 (mmt) REVERT: A 20 MET cc_start: 0.7577 (mmp) cc_final: 0.7295 (mmm) REVERT: C 11 LEU cc_start: 0.9103 (tp) cc_final: 0.8843 (tp) REVERT: C 304 GLU cc_start: 0.6810 (pp20) cc_final: 0.6285 (pp20) REVERT: D 58 MET cc_start: 0.8428 (tmm) cc_final: 0.8047 (tmm) REVERT: D 128 GLN cc_start: 0.7775 (tt0) cc_final: 0.7367 (mm-40) REVERT: E 90 LEU cc_start: 0.9343 (mt) cc_final: 0.8855 (tt) REVERT: E 282 TRP cc_start: 0.8449 (t-100) cc_final: 0.7977 (t-100) REVERT: F 8 MET cc_start: 0.5170 (tpt) cc_final: 0.4693 (tpp) REVERT: F 132 MET cc_start: 0.7863 (mtt) cc_final: 0.7590 (mtp) REVERT: F 205 TYR cc_start: 0.8049 (m-80) cc_final: 0.7415 (m-80) REVERT: G 229 LEU cc_start: 0.9262 (tp) cc_final: 0.8994 (tt) REVERT: G 422 GLN cc_start: 0.8874 (tt0) cc_final: 0.8671 (tp40) REVERT: G 495 GLU cc_start: 0.7829 (pt0) cc_final: 0.7626 (mm-30) REVERT: I 395 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7215 (m-80) outliers start: 9 outliers final: 4 residues processed: 290 average time/residue: 0.4256 time to fit residues: 196.6482 Evaluate side-chains 198 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 3.851 ------------------------------------------------------------------------------- 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: 0.8980 chunk 180 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 219 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 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: 1.5788 ------------------------------------------------------------------------------- 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** A 270 HIS ** 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 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: 0.7809 moved from start: 0.1272 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= 0.269 Angle : 0.731 10.574 42908 Z= 0.379 Chirality : 0.048 0.255 5136 Planarity : 0.005 0.070 5626 Dihedral : 6.824 85.823 4610 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 14.67 % Favored : 85.30 % Rotamer: Outliers : 0.07 % Allowed : 7.88 % Favored : 92.05 % 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: -4.78 (0.11), residues: 4287 helix: -1.79 (0.12), residues: 1405 sheet: -3.93 (0.18), residues: 489 loop : -4.06 (0.10), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 290 HIS 0.007 0.001 HIS C 160 PHE 0.019 0.002 PHE B 118 TYR 0.020 0.002 TYR E 38 ARG 0.007 0.000 ARG J 145 *********************** 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 278 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 276 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7500 (mmp) cc_final: 0.7150 (mmt) REVERT: A 20 MET cc_start: 0.7549 (mmp) cc_final: 0.7314 (mmm) REVERT: A 187 MET cc_start: 0.8337 (tpp) cc_final: 0.8072 (tpt) REVERT: C 44 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7776 (tm-30) REVERT: C 45 ILE cc_start: 0.8155 (mt) cc_final: 0.7676 (mt) REVERT: D 96 LEU cc_start: 0.9060 (tp) cc_final: 0.8829 (tp) REVERT: D 128 GLN cc_start: 0.7917 (tt0) cc_final: 0.7378 (pm20) REVERT: D 139 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7823 (tm-30) REVERT: D 166 MET cc_start: 0.7578 (mtm) cc_final: 0.7329 (mtp) REVERT: E 1 MET cc_start: 0.4263 (tpt) cc_final: 0.3834 (tpt) REVERT: E 90 LEU cc_start: 0.9274 (mt) cc_final: 0.8869 (tt) REVERT: E 216 MET cc_start: 0.7536 (tmm) cc_final: 0.6957 (tmm) REVERT: F 8 MET cc_start: 0.4922 (tpt) cc_final: 0.4382 (tpp) REVERT: F 132 MET cc_start: 0.7785 (mtt) cc_final: 0.7533 (mtp) REVERT: F 205 TYR cc_start: 0.7731 (m-80) cc_final: 0.7320 (m-80) REVERT: G 229 LEU cc_start: 0.9017 (tp) cc_final: 0.8190 (tt) REVERT: G 273 MET cc_start: 0.7861 (mtm) cc_final: 0.7068 (tpp) REVERT: G 422 GLN cc_start: 0.8663 (tt0) cc_final: 0.8375 (tp40) REVERT: H 273 MET cc_start: 0.8666 (mtm) cc_final: 0.8419 (mtm) REVERT: I 218 THR cc_start: 0.9151 (t) cc_final: 0.8942 (m) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 0.4501 time to fit residues: 205.9539 Evaluate side-chains 192 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 3.723 ------------------------------------------------------------------------------- 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: 2.9990 chunk 324 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 390 optimal weight: 40.0000 chunk 421 optimal weight: 5.9990 chunk 347 optimal weight: 8.9990 chunk 387 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 313 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 ASN E 190 HIS ** E 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 ASN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 281 ASN ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN I 263 ASN I 340 HIS ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31506 Z= 0.341 Angle : 0.756 11.363 42908 Z= 0.389 Chirality : 0.049 0.284 5136 Planarity : 0.005 0.061 5626 Dihedral : 6.733 87.421 4610 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 23.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 15.47 % Favored : 84.51 % Rotamer: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % 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: -4.26 (0.11), residues: 4287 helix: -1.22 (0.13), residues: 1403 sheet: -3.76 (0.19), residues: 497 loop : -3.81 (0.11), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 366 HIS 0.016 0.002 HIS I 214 PHE 0.020 0.002 PHE D 177 TYR 0.023 0.002 TYR E 38 ARG 0.007 0.001 ARG J 145 *********************** 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 262 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 3.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7776 (mmp) cc_final: 0.7424 (mmt) REVERT: A 20 MET cc_start: 0.7545 (mmp) cc_final: 0.7302 (mmm) REVERT: A 135 LEU cc_start: 0.8398 (mm) cc_final: 0.7887 (mm) REVERT: C 11 LEU cc_start: 0.9204 (tp) cc_final: 0.8992 (tp) REVERT: C 203 MET cc_start: 0.8572 (tpt) cc_final: 0.8135 (tpp) REVERT: D 96 LEU cc_start: 0.9047 (tp) cc_final: 0.8814 (tp) REVERT: D 128 GLN cc_start: 0.8024 (tt0) cc_final: 0.7154 (tp40) REVERT: D 139 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7633 (tm-30) REVERT: D 166 MET cc_start: 0.7610 (mtm) cc_final: 0.7377 (mtp) REVERT: E 44 GLU cc_start: 0.7968 (pt0) cc_final: 0.7687 (pt0) REVERT: E 216 MET cc_start: 0.7503 (tmm) cc_final: 0.7006 (tmm) REVERT: F 8 MET cc_start: 0.4613 (tpt) cc_final: 0.4110 (tpp) REVERT: F 205 TYR cc_start: 0.7863 (m-80) cc_final: 0.7398 (m-80) REVERT: G 443 PHE cc_start: 0.8747 (t80) cc_final: 0.8485 (t80) REVERT: G 448 GLN cc_start: 0.8098 (tt0) cc_final: 0.7890 (tp-100) REVERT: H 260 MET cc_start: 0.8453 (mmp) cc_final: 0.8149 (mmp) REVERT: H 273 MET cc_start: 0.8514 (mtm) cc_final: 0.8264 (mtm) REVERT: H 322 PHE cc_start: 0.7744 (t80) cc_final: 0.7533 (t80) REVERT: I 145 ARG cc_start: 0.7232 (ptm160) cc_final: 0.6910 (tmm-80) REVERT: I 181 MET cc_start: 0.7063 (ttt) cc_final: 0.6841 (ttt) REVERT: I 187 GLU cc_start: 0.8244 (tt0) cc_final: 0.7916 (tp30) REVERT: I 296 TYR cc_start: 0.8396 (t80) cc_final: 0.8141 (t80) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3807 time to fit residues: 167.2964 Evaluate side-chains 191 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.855 ------------------------------------------------------------------------------- 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: 2.9990 chunk 202 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 186 optimal weight: 20.0000 chunk 262 optimal weight: 0.5980 chunk 391 optimal weight: 5.9990 chunk 414 optimal weight: 0.0670 chunk 204 optimal weight: 0.9980 chunk 371 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 261 HIS ** 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 E 203 HIS ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 479 HIS H 194 GLN ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN I 333 GLN ** J 72 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31506 Z= 0.195 Angle : 0.670 11.796 42908 Z= 0.341 Chirality : 0.046 0.201 5136 Planarity : 0.005 0.066 5626 Dihedral : 6.161 87.867 4610 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.64 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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: -3.55 (0.12), residues: 4287 helix: -0.55 (0.14), residues: 1406 sheet: -3.46 (0.20), residues: 481 loop : -3.41 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 290 HIS 0.006 0.001 HIS D 125 PHE 0.028 0.002 PHE H 322 TYR 0.020 0.001 TYR H 214 ARG 0.008 0.000 ARG E 286 *********************** 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 308 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 3.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7633 (mmp) cc_final: 0.7266 (mmt) REVERT: A 20 MET cc_start: 0.7354 (mmp) cc_final: 0.7126 (mmm) REVERT: C 78 VAL cc_start: 0.8990 (m) cc_final: 0.8762 (p) REVERT: C 203 MET cc_start: 0.8430 (tpt) cc_final: 0.8002 (tpp) REVERT: D 96 LEU cc_start: 0.9004 (tp) cc_final: 0.8708 (tp) REVERT: D 128 GLN cc_start: 0.7969 (tt0) cc_final: 0.7512 (pm20) REVERT: D 139 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7533 (tm-30) REVERT: D 166 MET cc_start: 0.7344 (mtm) cc_final: 0.6871 (mtp) REVERT: D 226 MET cc_start: 0.8603 (tpt) cc_final: 0.8004 (tpt) REVERT: E 44 GLU cc_start: 0.7939 (pt0) cc_final: 0.7509 (pt0) REVERT: E 177 ASP cc_start: 0.7702 (p0) cc_final: 0.7392 (p0) REVERT: E 216 MET cc_start: 0.7471 (tmm) cc_final: 0.7096 (tmm) REVERT: F 8 MET cc_start: 0.4677 (tpt) cc_final: 0.4257 (tpp) REVERT: F 205 TYR cc_start: 0.7456 (m-80) cc_final: 0.7140 (m-80) REVERT: G 448 GLN cc_start: 0.7852 (tt0) cc_final: 0.7464 (tt0) REVERT: G 452 PHE cc_start: 0.7595 (m-10) cc_final: 0.7393 (m-80) REVERT: H 260 MET cc_start: 0.8603 (mmp) cc_final: 0.8073 (mmp) REVERT: I 296 TYR cc_start: 0.8286 (t80) cc_final: 0.8064 (t80) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.3982 time to fit residues: 202.8491 Evaluate side-chains 203 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 4.780 ------------------------------------------------------------------------------- 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: 7.9990 chunk 235 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 308 optimal weight: 0.0010 chunk 171 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 0.0870 chunk 372 optimal weight: 20.0000 chunk 104 optimal weight: 0.0870 overall best weight: 0.8144 ------------------------------------------------------------------------------- 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 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 GLN ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 HIS ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 GLN J 384 HIS J 434 GLN J 440 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2556 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= 0.193 Angle : 0.650 11.323 42908 Z= 0.330 Chirality : 0.046 0.248 5136 Planarity : 0.004 0.068 5626 Dihedral : 5.846 88.325 4610 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.12 % Favored : 89.85 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: -3.16 (0.12), residues: 4287 helix: -0.20 (0.14), residues: 1408 sheet: -3.27 (0.20), residues: 503 loop : -3.18 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 366 HIS 0.012 0.001 HIS I 214 PHE 0.019 0.002 PHE J 82 TYR 0.022 0.001 TYR C 344 ARG 0.008 0.000 ARG E 286 *********************** 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 299 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7540 (mmp) cc_final: 0.7195 (mmt) REVERT: A 20 MET cc_start: 0.7278 (mmp) cc_final: 0.7043 (mmm) REVERT: C 203 MET cc_start: 0.8420 (tpt) cc_final: 0.8048 (tpp) REVERT: D 96 LEU cc_start: 0.9047 (tp) cc_final: 0.8689 (tp) REVERT: D 128 GLN cc_start: 0.8071 (tt0) cc_final: 0.7549 (pm20) REVERT: D 139 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7357 (tm-30) REVERT: D 166 MET cc_start: 0.7114 (mtm) cc_final: 0.6763 (mtp) REVERT: E 1 MET cc_start: 0.6153 (ttp) cc_final: 0.5948 (ttp) REVERT: E 44 GLU cc_start: 0.7896 (pt0) cc_final: 0.7467 (pt0) REVERT: F 8 MET cc_start: 0.4692 (tpt) cc_final: 0.4405 (tpp) REVERT: F 86 THR cc_start: 0.5652 (p) cc_final: 0.5335 (p) REVERT: F 205 TYR cc_start: 0.7271 (m-80) cc_final: 0.6962 (m-80) REVERT: H 196 MET cc_start: 0.7930 (ppp) cc_final: 0.7618 (ppp) REVERT: H 260 MET cc_start: 0.8608 (mmp) cc_final: 0.8099 (mmp) REVERT: H 273 MET cc_start: 0.8733 (mtm) cc_final: 0.8436 (mtm) REVERT: H 274 HIS cc_start: 0.6778 (m-70) cc_final: 0.6474 (m-70) REVERT: I 296 TYR cc_start: 0.8161 (t80) cc_final: 0.7834 (t80) REVERT: I 426 LYS cc_start: 0.8423 (mttm) cc_final: 0.7914 (mttm) REVERT: J 321 LEU cc_start: 0.8495 (mp) cc_final: 0.7778 (mp) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3857 time to fit residues: 190.4976 Evaluate side-chains 205 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 3.468 ------------------------------------------------------------------------------- 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: 9.9990 chunk 81 optimal weight: 0.6980 chunk 243 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 415 optimal weight: 40.0000 chunk 344 optimal weight: 30.0000 chunk 192 optimal weight: 0.0020 chunk 34 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 132 ASN D 280 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN F 32 ASN G 265 GLN ** G 475 ASN ** 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** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 388 ASN J 434 GLN J 440 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31506 Z= 0.186 Angle : 0.642 11.257 42908 Z= 0.323 Chirality : 0.045 0.224 5136 Planarity : 0.004 0.070 5626 Dihedral : 5.627 88.803 4610 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.38 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: -2.85 (0.13), residues: 4287 helix: 0.06 (0.14), residues: 1402 sheet: -3.07 (0.20), residues: 522 loop : -2.97 (0.12), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 290 HIS 0.006 0.001 HIS J 168 PHE 0.027 0.002 PHE A 250 TYR 0.021 0.001 TYR E 94 ARG 0.005 0.000 ARG B 74 *********************** 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 294 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7404 (mmp) cc_final: 0.7192 (mmt) REVERT: A 20 MET cc_start: 0.7371 (mmp) cc_final: 0.7087 (mmm) REVERT: B 279 SER cc_start: 0.9084 (m) cc_final: 0.8824 (t) REVERT: C 203 MET cc_start: 0.8354 (tpt) cc_final: 0.7998 (tpp) REVERT: D 96 LEU cc_start: 0.9052 (tp) cc_final: 0.8659 (tp) REVERT: D 128 GLN cc_start: 0.8073 (tt0) cc_final: 0.7565 (pm20) REVERT: D 139 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7297 (tm-30) REVERT: D 166 MET cc_start: 0.7026 (mtm) cc_final: 0.6659 (mtp) REVERT: E 1 MET cc_start: 0.5146 (ttp) cc_final: 0.4738 (ttp) REVERT: E 38 TYR cc_start: 0.7434 (m-80) cc_final: 0.7137 (m-80) REVERT: E 115 HIS cc_start: 0.7873 (p-80) cc_final: 0.7530 (p-80) REVERT: E 204 LEU cc_start: 0.8874 (tp) cc_final: 0.8634 (tt) REVERT: F 8 MET cc_start: 0.4623 (tpt) cc_final: 0.4254 (tpp) REVERT: F 84 MET cc_start: 0.4299 (ppp) cc_final: 0.2427 (mtt) REVERT: F 86 THR cc_start: 0.5550 (p) cc_final: 0.5264 (p) REVERT: F 109 ILE cc_start: 0.8438 (mp) cc_final: 0.8140 (mm) REVERT: F 205 TYR cc_start: 0.7259 (m-80) cc_final: 0.6952 (m-80) REVERT: G 415 MET cc_start: 0.9314 (tmm) cc_final: 0.9045 (tmm) REVERT: H 196 MET cc_start: 0.7907 (ppp) cc_final: 0.7577 (ppp) REVERT: H 254 ASN cc_start: 0.8525 (t0) cc_final: 0.8245 (t0) REVERT: H 273 MET cc_start: 0.8698 (mtm) cc_final: 0.8310 (mtm) REVERT: H 274 HIS cc_start: 0.6650 (m-70) cc_final: 0.6336 (m-70) REVERT: H 422 GLN cc_start: 0.8480 (mt0) cc_final: 0.8141 (mt0) REVERT: I 228 LEU cc_start: 0.8692 (tp) cc_final: 0.8471 (tt) REVERT: I 296 TYR cc_start: 0.7995 (t80) cc_final: 0.7515 (t80) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.3670 time to fit residues: 182.0303 Evaluate side-chains 202 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 3.466 ------------------------------------------------------------------------------- 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: 0.5980 chunk 46 optimal weight: 0.7980 chunk 236 optimal weight: 8.9990 chunk 303 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 349 optimal weight: 10.0000 chunk 231 optimal weight: 0.4980 chunk 413 optimal weight: 30.0000 chunk 258 optimal weight: 0.4980 chunk 252 optimal weight: 7.9990 chunk 190 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 HIS G 477 GLN ** H 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 431 ASN ** 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 72 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31506 Z= 0.174 Angle : 0.629 10.743 42908 Z= 0.316 Chirality : 0.045 0.258 5136 Planarity : 0.004 0.071 5626 Dihedral : 5.440 89.548 4610 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.75 % Favored : 91.23 % Rotamer: Outliers : 0.03 % Allowed : 2.05 % Favored : 97.92 % 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: -2.64 (0.13), residues: 4287 helix: 0.20 (0.14), residues: 1411 sheet: -3.04 (0.20), residues: 532 loop : -2.80 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 366 HIS 0.006 0.001 HIS I 290 PHE 0.019 0.001 PHE A 72 TYR 0.029 0.001 TYR H 214 ARG 0.005 0.000 ARG E 286 *********************** 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 292 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7317 (mmp) cc_final: 0.7021 (mmt) REVERT: A 20 MET cc_start: 0.7117 (mmp) cc_final: 0.6655 (mmm) REVERT: B 279 SER cc_start: 0.9073 (m) cc_final: 0.8804 (t) REVERT: C 60 LEU cc_start: 0.8926 (tt) cc_final: 0.8682 (tp) REVERT: C 203 MET cc_start: 0.8300 (tpt) cc_final: 0.7974 (tpp) REVERT: D 96 LEU cc_start: 0.9059 (tp) cc_final: 0.8642 (tp) REVERT: D 139 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7398 (tm-30) REVERT: D 166 MET cc_start: 0.7000 (mtm) cc_final: 0.6670 (mtp) REVERT: E 1 MET cc_start: 0.5081 (ttp) cc_final: 0.4710 (ttp) REVERT: E 8 MET cc_start: 0.8327 (ttm) cc_final: 0.8093 (ttm) REVERT: E 38 TYR cc_start: 0.7285 (m-80) cc_final: 0.7046 (m-80) REVERT: E 115 HIS cc_start: 0.7832 (p-80) cc_final: 0.7487 (p-80) REVERT: E 204 LEU cc_start: 0.8901 (tp) cc_final: 0.8638 (tt) REVERT: F 84 MET cc_start: 0.3948 (ppp) cc_final: 0.2631 (mtt) REVERT: F 109 ILE cc_start: 0.8406 (mp) cc_final: 0.8155 (mm) REVERT: F 205 TYR cc_start: 0.7241 (m-80) cc_final: 0.6935 (m-80) REVERT: F 216 MET cc_start: 0.8351 (tpp) cc_final: 0.8131 (tpp) REVERT: F 290 TRP cc_start: 0.7268 (t60) cc_final: 0.6667 (t60) REVERT: H 196 MET cc_start: 0.7922 (ppp) cc_final: 0.7694 (ppp) REVERT: H 254 ASN cc_start: 0.8561 (t0) cc_final: 0.8299 (t0) REVERT: H 260 MET cc_start: 0.8318 (mmp) cc_final: 0.7497 (mmp) REVERT: H 273 MET cc_start: 0.8628 (mtm) cc_final: 0.8314 (mtt) REVERT: H 274 HIS cc_start: 0.6760 (m-70) cc_final: 0.6449 (m-70) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.3856 time to fit residues: 189.6071 Evaluate side-chains 208 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 3.788 ------------------------------------------------------------------------------- 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: 2.9990 chunk 165 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 81 optimal weight: 0.0010 chunk 80 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 281 optimal weight: 4.9990 chunk 204 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 325 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 477 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** ** J 72 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: 0.7624 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31506 Z= 0.175 Angle : 0.623 11.762 42908 Z= 0.313 Chirality : 0.045 0.233 5136 Planarity : 0.004 0.072 5626 Dihedral : 5.310 89.747 4610 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.72 % Favored : 91.25 % Rotamer: Outliers : 0.03 % Allowed : 1.49 % Favored : 98.47 % 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: -2.48 (0.13), residues: 4287 helix: 0.32 (0.14), residues: 1411 sheet: -2.78 (0.20), residues: 567 loop : -2.73 (0.12), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 290 HIS 0.005 0.001 HIS C 160 PHE 0.029 0.001 PHE H 452 TYR 0.022 0.001 TYR H 214 ARG 0.004 0.000 ARG E 286 *********************** 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 289 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 288 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4586 (mpp) cc_final: 0.3588 (mpt) REVERT: A 20 MET cc_start: 0.6834 (mmp) cc_final: 0.6474 (mmm) REVERT: B 279 SER cc_start: 0.9109 (m) cc_final: 0.8861 (t) REVERT: C 60 LEU cc_start: 0.8901 (tt) cc_final: 0.8691 (tp) REVERT: C 203 MET cc_start: 0.8417 (tpt) cc_final: 0.8086 (tpp) REVERT: D 34 MET cc_start: 0.8550 (mmm) cc_final: 0.8325 (tpp) REVERT: D 96 LEU cc_start: 0.9126 (tp) cc_final: 0.8645 (tp) REVERT: D 139 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7451 (tm-30) REVERT: D 166 MET cc_start: 0.7135 (mtm) cc_final: 0.6919 (mtp) REVERT: D 277 GLN cc_start: 0.7911 (mm110) cc_final: 0.7520 (mm110) REVERT: D 301 ASP cc_start: 0.7688 (t70) cc_final: 0.7100 (t0) REVERT: E 1 MET cc_start: 0.4639 (ttp) cc_final: 0.4299 (ttp) REVERT: E 8 MET cc_start: 0.8181 (ttm) cc_final: 0.7861 (ttm) REVERT: E 38 TYR cc_start: 0.7760 (m-80) cc_final: 0.7299 (m-10) REVERT: E 115 HIS cc_start: 0.7780 (p-80) cc_final: 0.7377 (p-80) REVERT: E 204 LEU cc_start: 0.8813 (tp) cc_final: 0.8496 (tt) REVERT: F 8 MET cc_start: 0.4111 (tpt) cc_final: 0.3894 (tpp) REVERT: F 86 THR cc_start: 0.5539 (p) cc_final: 0.5129 (p) REVERT: F 109 ILE cc_start: 0.8428 (mp) cc_final: 0.8162 (mm) REVERT: F 205 TYR cc_start: 0.7292 (m-80) cc_final: 0.6980 (m-80) REVERT: F 290 TRP cc_start: 0.7402 (t60) cc_final: 0.6715 (t60) REVERT: H 196 MET cc_start: 0.7946 (ppp) cc_final: 0.7700 (ppp) REVERT: H 254 ASN cc_start: 0.8462 (t0) cc_final: 0.8217 (t0) REVERT: H 260 MET cc_start: 0.8312 (mmp) cc_final: 0.7732 (mmp) REVERT: H 273 MET cc_start: 0.8690 (mtm) cc_final: 0.8376 (mtm) REVERT: H 274 HIS cc_start: 0.6997 (m-70) cc_final: 0.6662 (m-70) REVERT: H 422 GLN cc_start: 0.8286 (mt0) cc_final: 0.7890 (mt0) REVERT: I 228 LEU cc_start: 0.8317 (tt) cc_final: 0.8063 (mm) REVERT: J 191 SER cc_start: 0.7880 (m) cc_final: 0.7648 (t) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.3745 time to fit residues: 182.7326 Evaluate side-chains 213 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.362 ------------------------------------------------------------------------------- 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: 1.9990 chunk 396 optimal weight: 0.9980 chunk 361 optimal weight: 20.0000 chunk 385 optimal weight: 20.0000 chunk 231 optimal weight: 0.0570 chunk 167 optimal weight: 3.9990 chunk 302 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 348 optimal weight: 20.0000 chunk 364 optimal weight: 0.6980 chunk 383 optimal weight: 9.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** 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 72 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31506 Z= 0.198 Angle : 0.630 9.721 42908 Z= 0.316 Chirality : 0.046 0.253 5136 Planarity : 0.004 0.072 5626 Dihedral : 5.308 89.053 4610 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.24 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -2.43 (0.13), residues: 4287 helix: 0.37 (0.14), residues: 1413 sheet: -2.83 (0.20), residues: 553 loop : -2.69 (0.12), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP H 366 HIS 0.006 0.001 HIS I 214 PHE 0.017 0.001 PHE H 452 TYR 0.020 0.001 TYR H 214 ARG 0.006 0.000 ARG H 321 *********************** 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 278 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4390 (mpp) cc_final: 0.3506 (mpt) REVERT: A 20 MET cc_start: 0.7087 (mmp) cc_final: 0.6770 (mmm) REVERT: B 93 MET cc_start: 0.8120 (tpp) cc_final: 0.7836 (mmt) REVERT: C 203 MET cc_start: 0.8287 (tpt) cc_final: 0.7970 (tpp) REVERT: D 96 LEU cc_start: 0.9153 (tp) cc_final: 0.8679 (tp) REVERT: D 139 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7521 (tm-30) REVERT: D 166 MET cc_start: 0.7181 (mtm) cc_final: 0.6935 (mtp) REVERT: D 277 GLN cc_start: 0.7980 (mm110) cc_final: 0.7610 (mm110) REVERT: D 301 ASP cc_start: 0.7695 (t70) cc_final: 0.7019 (t0) REVERT: E 1 MET cc_start: 0.4592 (ttp) cc_final: 0.4282 (ttp) REVERT: E 38 TYR cc_start: 0.7698 (m-80) cc_final: 0.7424 (m-80) REVERT: E 204 LEU cc_start: 0.8845 (tp) cc_final: 0.8551 (tt) REVERT: F 8 MET cc_start: 0.4232 (tpt) cc_final: 0.3670 (tpp) REVERT: F 84 MET cc_start: 0.4309 (ppp) cc_final: 0.2582 (mtt) REVERT: F 86 THR cc_start: 0.5340 (p) cc_final: 0.4887 (p) REVERT: F 109 ILE cc_start: 0.8468 (mp) cc_final: 0.8219 (mm) REVERT: F 205 TYR cc_start: 0.7324 (m-80) cc_final: 0.6993 (m-80) REVERT: F 290 TRP cc_start: 0.7302 (t60) cc_final: 0.6591 (t60) REVERT: H 196 MET cc_start: 0.7988 (ppp) cc_final: 0.7744 (ppp) REVERT: H 254 ASN cc_start: 0.8571 (t0) cc_final: 0.8305 (t0) REVERT: H 260 MET cc_start: 0.8350 (mmp) cc_final: 0.8125 (mmp) REVERT: H 273 MET cc_start: 0.8546 (mtm) cc_final: 0.8262 (mtm) REVERT: H 274 HIS cc_start: 0.7103 (m-70) cc_final: 0.6757 (m-70) REVERT: H 422 GLN cc_start: 0.8351 (mt0) cc_final: 0.7920 (mt0) REVERT: I 228 LEU cc_start: 0.8344 (tt) cc_final: 0.8079 (mm) REVERT: J 43 LEU cc_start: 0.8633 (pt) cc_final: 0.8382 (pp) REVERT: J 191 SER cc_start: 0.7885 (m) cc_final: 0.7669 (t) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3933 time to fit residues: 184.0958 Evaluate side-chains 212 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.375 ------------------------------------------------------------------------------- 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: 0.0670 chunk 407 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 427 optimal weight: 30.0000 chunk 393 optimal weight: 30.0000 chunk 340 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 262 optimal weight: 0.2980 chunk 208 optimal weight: 0.0370 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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** ** F 4 GLN ** 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 304 HIS J 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31506 Z= 0.179 Angle : 0.630 13.350 42908 Z= 0.314 Chirality : 0.045 0.248 5136 Planarity : 0.004 0.072 5626 Dihedral : 5.250 89.023 4610 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.65 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -2.30 (0.13), residues: 4287 helix: 0.43 (0.14), residues: 1404 sheet: -2.74 (0.21), residues: 546 loop : -2.58 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 290 HIS 0.005 0.001 HIS C 160 PHE 0.017 0.001 PHE H 452 TYR 0.025 0.001 TYR E 94 ARG 0.003 0.000 ARG I 269 ********************** 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 286 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.7172 (mmp) cc_final: 0.6898 (mmm) REVERT: B 93 MET cc_start: 0.8106 (tpp) cc_final: 0.7877 (mmt) REVERT: C 203 MET cc_start: 0.8367 (tpt) cc_final: 0.8074 (tpp) REVERT: D 96 LEU cc_start: 0.9155 (tp) cc_final: 0.8702 (tp) REVERT: D 139 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7550 (tm-30) REVERT: D 167 THR cc_start: 0.8256 (p) cc_final: 0.7938 (p) REVERT: D 203 MET cc_start: 0.8032 (mmm) cc_final: 0.7343 (mmm) REVERT: D 277 GLN cc_start: 0.7906 (mm110) cc_final: 0.7570 (mm110) REVERT: D 301 ASP cc_start: 0.7891 (t70) cc_final: 0.7185 (t0) REVERT: E 1 MET cc_start: 0.4454 (ttp) cc_final: 0.4105 (ttp) REVERT: E 8 MET cc_start: 0.8085 (ttm) cc_final: 0.7814 (ttm) REVERT: F 8 MET cc_start: 0.3859 (tpt) cc_final: 0.3397 (tpp) REVERT: F 84 MET cc_start: 0.4113 (ppp) cc_final: 0.2618 (mtt) REVERT: F 86 THR cc_start: 0.5377 (p) cc_final: 0.4967 (p) REVERT: F 109 ILE cc_start: 0.8422 (mp) cc_final: 0.8167 (mm) REVERT: F 205 TYR cc_start: 0.7282 (m-80) cc_final: 0.6898 (m-80) REVERT: F 290 TRP cc_start: 0.7321 (t60) cc_final: 0.6563 (t60) REVERT: H 196 MET cc_start: 0.7925 (ppp) cc_final: 0.7675 (ppp) REVERT: H 254 ASN cc_start: 0.8681 (t0) cc_final: 0.8362 (t0) REVERT: H 273 MET cc_start: 0.8710 (mtm) cc_final: 0.8374 (mtm) REVERT: H 274 HIS cc_start: 0.7096 (m-70) cc_final: 0.6744 (m-70) REVERT: H 422 GLN cc_start: 0.8241 (mt0) cc_final: 0.7802 (mt0) REVERT: I 228 LEU cc_start: 0.8286 (tt) cc_final: 0.8051 (mm) REVERT: J 303 LEU cc_start: 0.8379 (tt) cc_final: 0.7979 (tt) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3866 time to fit residues: 184.9057 Evaluate side-chains 214 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 3.659 ------------------------------------------------------------------------------- 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: 4.9990 chunk 362 optimal weight: 40.0000 chunk 104 optimal weight: 0.8980 chunk 313 optimal weight: 3.9990 chunk 50 optimal weight: 0.0670 chunk 94 optimal weight: 6.9990 chunk 340 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 350 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- 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** D 280 ASN ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN ** G 422 GLN ** 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 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 304 HIS J 440 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.087108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.069965 restraints weight = 118949.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.070585 restraints weight = 85241.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071064 restraints weight = 63453.763| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 31506 Z= 0.328 Angle : 0.714 11.425 42908 Z= 0.362 Chirality : 0.048 0.278 5136 Planarity : 0.005 0.071 5626 Dihedral : 5.679 85.013 4610 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.97 % Favored : 88.01 % 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: -2.53 (0.13), residues: 4287 helix: 0.20 (0.14), residues: 1406 sheet: -2.76 (0.21), residues: 542 loop : -2.72 (0.12), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP H 366 HIS 0.008 0.002 HIS D 188 PHE 0.029 0.002 PHE A 10 TYR 0.026 0.002 TYR H 214 ARG 0.007 0.001 ARG H 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5053.86 seconds wall clock time: 93 minutes 23.28 seconds (5603.28 seconds total)