Starting phenix.real_space_refine on Sun Mar 17 04:47:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo2_20142/03_2024/6oo2_20142_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo2_20142/03_2024/6oo2_20142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo2_20142/03_2024/6oo2_20142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo2_20142/03_2024/6oo2_20142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo2_20142/03_2024/6oo2_20142_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo2_20142/03_2024/6oo2_20142_updated.pdb" } resolution = 4.4 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= 0.003 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 45 5.16 5 Be 3 3.05 5 C 10334 2.51 5 N 2982 2.21 5 O 3304 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D GLU 392": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 247": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16691 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2427 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2482 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 304} Chain breaks: 1 Chain: "D" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2482 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 304} Chain breaks: 1 Chain: "E" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2351 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 286} Chain breaks: 1 Chain: "G" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 119 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 19} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 1498 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 287} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 902 Unresolved non-hydrogen angles: 1146 Unresolved non-hydrogen dihedrals: 745 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 16, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 12, 'GLU:plan': 24, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 448 Chain: "H" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "I" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "J" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "K" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "M" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "N" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "O" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "P" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "Q" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "R" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "S" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 210 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.59, per 1000 atoms: 0.57 Number of scatterers: 16691 At special positions: 0 Unit cell: (81.75, 161.32, 155.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 45 16.00 P 10 15.00 Mg 4 11.99 F 9 9.00 O 3304 8.00 N 2982 7.00 C 10334 6.00 Be 3 4.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.82 Conformation dependent library (CDL) restraints added in 3.5 seconds 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4598 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 13 sheets defined 54.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.739A pdb=" N SER A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 121 " --> pdb=" O ALA A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 121' Processing helix chain 'A' and resid 139 through 154 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'A' and resid 209 through 223 removed outlier: 4.005A pdb=" N VAL A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 246 through 259 removed outlier: 4.709A pdb=" N ARG A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 336 through 355 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 419 through 432 Processing helix chain 'B' and resid 113 through 122 removed outlier: 4.440A pdb=" N SER B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 151 through 154 No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing helix chain 'B' and resid 179 through 189 Processing helix chain 'B' and resid 209 through 223 removed outlier: 4.313A pdb=" N VAL B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 336 through 355 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'C' and resid 113 through 119 Processing helix chain 'C' and resid 139 through 154 Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'C' and resid 210 through 223 removed outlier: 3.588A pdb=" N VAL C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 260 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'C' and resid 336 through 355 Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'D' and resid 113 through 122 removed outlier: 4.659A pdb=" N SER D 121 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 139 through 154 Proline residue: D 152 - end of helix Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 199 through 202 No H-bonds generated for 'chain 'D' and resid 199 through 202' Processing helix chain 'D' and resid 210 through 223 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 336 through 355 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 403 through 412 Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'E' and resid 139 through 154 Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 179 through 189 Processing helix chain 'E' and resid 200 through 202 No H-bonds generated for 'chain 'E' and resid 200 through 202' Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 234 through 237 No H-bonds generated for 'chain 'E' and resid 234 through 237' Processing helix chain 'E' and resid 246 through 260 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 321 through 330 Processing helix chain 'E' and resid 336 through 355 Proline residue: E 350 - end of helix removed outlier: 3.557A pdb=" N GLN E 355 " --> pdb=" O ILE E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 139 through 154 Proline residue: F 152 - end of helix Processing helix chain 'F' and resid 156 through 159 Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 207 through 224 removed outlier: 3.645A pdb=" N GLU F 211 " --> pdb=" O GLY F 208 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU F 217 " --> pdb=" O VAL F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 263 removed outlier: 3.555A pdb=" N LEU F 256 " --> pdb=" O ILE F 252 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL F 258 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL F 263 " --> pdb=" O GLN F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 281 No H-bonds generated for 'chain 'F' and resid 279 through 281' Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.577A pdb=" N ARG F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 321 through 331 Processing helix chain 'F' and resid 336 through 355 removed outlier: 3.936A pdb=" N MET F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Proline residue: F 350 - end of helix Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 403 through 412 removed outlier: 3.511A pdb=" N LEU F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 432 removed outlier: 3.661A pdb=" N LEU F 422 " --> pdb=" O GLU F 419 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN F 425 " --> pdb=" O LEU F 422 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN F 427 " --> pdb=" O LYS F 424 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE F 432 " --> pdb=" O THR F 429 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 310 removed outlier: 3.510A pdb=" N GLN H 298 " --> pdb=" O ILE H 294 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR H 310 " --> pdb=" O SER H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 329 removed outlier: 3.837A pdb=" N THR H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 310 removed outlier: 4.430A pdb=" N TYR I 310 " --> pdb=" O SER I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 329 removed outlier: 3.837A pdb=" N THR I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 291 through 310 removed outlier: 4.428A pdb=" N TYR J 310 " --> pdb=" O SER J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 329 removed outlier: 3.839A pdb=" N THR J 321 " --> pdb=" O LYS J 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 310 removed outlier: 4.431A pdb=" N TYR K 310 " --> pdb=" O SER K 306 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 329 removed outlier: 3.839A pdb=" N THR K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 310 removed outlier: 3.585A pdb=" N GLN L 298 " --> pdb=" O ILE L 294 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS L 299 " --> pdb=" O GLU L 295 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR L 310 " --> pdb=" O SER L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 329 removed outlier: 3.839A pdb=" N THR L 321 " --> pdb=" O LYS L 317 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 310 removed outlier: 4.431A pdb=" N TYR M 310 " --> pdb=" O SER M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 329 removed outlier: 3.708A pdb=" N THR M 321 " --> pdb=" O LYS M 317 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 310 removed outlier: 4.426A pdb=" N TYR N 310 " --> pdb=" O SER N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 329 removed outlier: 3.682A pdb=" N THR N 321 " --> pdb=" O LYS N 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 282 through 310 removed outlier: 4.422A pdb=" N TYR O 310 " --> pdb=" O SER O 306 " (cutoff:3.500A) Processing helix chain 'O' and resid 313 through 329 removed outlier: 3.839A pdb=" N THR O 321 " --> pdb=" O LYS O 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 291 through 310 removed outlier: 3.850A pdb=" N ILE P 297 " --> pdb=" O LYS P 293 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLN P 298 " --> pdb=" O ILE P 294 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR P 310 " --> pdb=" O SER P 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 313 through 329 removed outlier: 3.693A pdb=" N THR P 321 " --> pdb=" O LYS P 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 282 through 310 removed outlier: 4.436A pdb=" N TYR Q 310 " --> pdb=" O SER Q 306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 313 through 329 removed outlier: 3.688A pdb=" N THR Q 321 " --> pdb=" O LYS Q 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 310 removed outlier: 4.426A pdb=" N TYR R 310 " --> pdb=" O SER R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 329 removed outlier: 3.722A pdb=" N THR R 321 " --> pdb=" O LYS R 317 " (cutoff:3.500A) Processing helix chain 'S' and resid 290 through 310 removed outlier: 4.433A pdb=" N TYR S 310 " --> pdb=" O SER S 306 " (cutoff:3.500A) Processing helix chain 'S' and resid 313 through 329 removed outlier: 3.698A pdb=" N THR S 321 " --> pdb=" O LYS S 317 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 169 through 173 removed outlier: 6.542A pdb=" N ARG A 292 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N TYR A 172 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 294 " --> pdb=" O TYR A 172 " (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 197 Processing sheet with id= C, first strand: chain 'A' and resid 360 through 363 removed outlier: 4.037A pdb=" N LYS A 372 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 293 through 296 removed outlier: 6.213A pdb=" N LEU B 170 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE B 296 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR B 172 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 173 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 275 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE B 230 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE B 195 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 232 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 197 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 360 through 362 Processing sheet with id= F, first strand: chain 'C' and resid 292 through 296 removed outlier: 3.640A pdb=" N ARG C 292 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE C 169 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 272 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 171 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY C 274 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLY C 173 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR C 276 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER C 227 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU C 273 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ALA C 275 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE C 231 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR C 193 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE C 230 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE C 195 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP C 232 " --> pdb=" O PHE C 195 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 197 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 360 through 362 Processing sheet with id= H, first strand: chain 'D' and resid 292 through 296 removed outlier: 3.570A pdb=" N GLY D 173 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N SER D 227 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU D 273 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE D 229 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA D 275 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE D 231 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR D 193 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE D 230 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE D 195 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP D 232 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 197 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 360 through 363 removed outlier: 3.597A pdb=" N VAL D 363 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS D 372 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 292 through 296 removed outlier: 6.663A pdb=" N SER E 227 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU E 273 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE E 229 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA E 275 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 231 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR E 193 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE E 230 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE E 195 " --> pdb=" O PHE E 230 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP E 232 " --> pdb=" O PHE E 195 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 360 through 363 removed outlier: 4.256A pdb=" N LYS E 372 " --> pdb=" O VAL E 363 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 124 through 126 removed outlier: 6.832A pdb=" N ARG F 292 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N TYR F 172 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE F 294 " --> pdb=" O TYR F 172 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 383 through 385 removed outlier: 4.076A pdb=" N LYS F 372 " --> pdb=" O VAL F 363 " (cutoff:3.500A) 911 hydrogen bonds defined for protein. 2655 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: 5.23 Time building geometry restraints manager: 7.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3009 1.32 - 1.44: 3847 1.44 - 1.56: 9906 1.56 - 1.69: 40 1.69 - 1.81: 80 Bond restraints: 16882 Sorted by residual: bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" CA ILE J 305 " pdb=" CB ILE J 305 " ideal model delta sigma weight residual 1.538 1.588 -0.049 1.06e-02 8.90e+03 2.14e+01 bond pdb=" CA ILE R 305 " pdb=" CB ILE R 305 " ideal model delta sigma weight residual 1.538 1.587 -0.049 1.06e-02 8.90e+03 2.10e+01 ... (remaining 16877 not shown) Histogram of bond angle deviations from ideal: 99.93 - 107.14: 546 107.14 - 114.35: 9884 114.35 - 121.56: 8168 121.56 - 128.78: 4312 128.78 - 135.99: 80 Bond angle restraints: 22990 Sorted by residual: angle pdb=" N ASN Q 328 " pdb=" CA ASN Q 328 " pdb=" C ASN Q 328 " ideal model delta sigma weight residual 113.50 105.26 8.24 1.23e+00 6.61e-01 4.49e+01 angle pdb=" N ASN M 328 " pdb=" CA ASN M 328 " pdb=" C ASN M 328 " ideal model delta sigma weight residual 113.50 105.31 8.19 1.23e+00 6.61e-01 4.44e+01 angle pdb=" N ASN K 328 " pdb=" CA ASN K 328 " pdb=" C ASN K 328 " ideal model delta sigma weight residual 113.50 105.33 8.17 1.23e+00 6.61e-01 4.42e+01 angle pdb=" N ASN O 328 " pdb=" CA ASN O 328 " pdb=" C ASN O 328 " ideal model delta sigma weight residual 113.50 105.34 8.16 1.23e+00 6.61e-01 4.40e+01 angle pdb=" N ASN S 328 " pdb=" CA ASN S 328 " pdb=" C ASN S 328 " ideal model delta sigma weight residual 113.50 105.37 8.13 1.23e+00 6.61e-01 4.36e+01 ... (remaining 22985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 10060 33.70 - 67.40: 162 67.40 - 101.11: 15 101.11 - 134.81: 2 134.81 - 168.51: 4 Dihedral angle restraints: 10243 sinusoidal: 3204 harmonic: 7039 Sorted by residual: dihedral pdb=" C5' ADP B 501 " pdb=" O5' ADP B 501 " pdb=" PA ADP B 501 " pdb=" O2A ADP B 501 " ideal model delta sinusoidal sigma weight residual 300.00 131.49 168.51 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual 300.00 136.64 163.37 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 88.99 -148.99 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 10240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2141 0.073 - 0.147: 470 0.147 - 0.220: 130 0.220 - 0.294: 27 0.294 - 0.367: 5 Chirality restraints: 2773 Sorted by residual: chirality pdb=" CA ILE F 278 " pdb=" N ILE F 278 " pdb=" C ILE F 278 " pdb=" CB ILE F 278 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA ASP F 394 " pdb=" N ASP F 394 " pdb=" C ASP F 394 " pdb=" CB ASP F 394 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA MET F 386 " pdb=" N MET F 386 " pdb=" C MET F 386 " pdb=" CB MET F 386 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 2770 not shown) Planarity restraints: 3027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 379 " -0.023 2.00e-02 2.50e+03 4.80e-02 2.30e+01 pdb=" C GLY F 379 " 0.083 2.00e-02 2.50e+03 pdb=" O GLY F 379 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP F 380 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 237 " 0.023 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C LEU F 237 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU F 237 " 0.031 2.00e-02 2.50e+03 pdb=" N THR F 238 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 297 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C PRO F 297 " -0.073 2.00e-02 2.50e+03 pdb=" O PRO F 297 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU F 298 " 0.024 2.00e-02 2.50e+03 ... (remaining 3024 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 257 2.61 - 3.18: 14447 3.18 - 3.75: 26010 3.75 - 4.33: 33077 4.33 - 4.90: 54816 Nonbonded interactions: 128607 Sorted by model distance: nonbonded pdb=" OG SER A 180 " pdb="MG MG A 503 " model vdw 2.037 2.170 nonbonded pdb=" OG SER C 180 " pdb="MG MG C 503 " model vdw 2.038 2.170 nonbonded pdb=" OG SER B 180 " pdb="MG MG B 503 " model vdw 2.038 2.170 nonbonded pdb=" O2B ADP A 501 " pdb="MG MG A 503 " model vdw 2.038 2.170 nonbonded pdb=" F1 BEF C 502 " pdb="MG MG C 503 " model vdw 2.038 2.120 ... (remaining 128602 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 126 through 136 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 139 and (name N or name CA or \ name C or name O or name CB )) or (resid 140 through 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 and (name N or name CA or name C or name O or name \ CB )) or resid 178 or (resid 179 through 207 and (name N or name CA or name C o \ r name O or name CB )) or resid 208 or (resid 209 through 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 24 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 244 or (resi \ d 245 through 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) o \ r resid 264 or (resid 265 and (name N or name CA or name C or name O or name CB \ )) or (resid 268 and (name N or name CA or name C or name O or name CB )) or res \ id 269 or (resid 270 through 273 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 274 through 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 or (resid 314 through 327 and (name N or name CA or na \ me C or name O or name CB )) or (resid 328 through 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (name \ N or name CA or name C or name O or name CB )) or resid 336 or (resid 337 throu \ gh 364 and (name N or name CA or name C or name O or name CB )) or (resid 371 th \ rough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 through 381 and (name N or name CA or name C or name O or name CB \ )) or (resid 382 through 432 and (name N or name CA or name C or name O or name \ CB )) or resid 433)) selection = (chain 'B' and ((resid 126 through 136 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 139 and (name N or name CA or \ name C or name O or name CB )) or (resid 140 through 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 and (name N or name CA or name C or name O or name \ CB )) or resid 178 or (resid 179 through 207 and (name N or name CA or name C o \ r name O or name CB )) or resid 208 or (resid 209 through 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 24 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 244 or (resi \ d 245 through 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) o \ r resid 264 or (resid 265 and (name N or name CA or name C or name O or name CB \ )) or (resid 268 and (name N or name CA or name C or name O or name CB )) or res \ id 269 or (resid 270 through 273 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 274 through 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 or (resid 314 through 327 and (name N or name CA or na \ me C or name O or name CB )) or (resid 328 through 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (name \ N or name CA or name C or name O or name CB )) or resid 336 or (resid 337 throu \ gh 364 and (name N or name CA or name C or name O or name CB )) or (resid 371 th \ rough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 through 381 and (name N or name CA or name C or name O or name CB \ )) or (resid 382 through 432 and (name N or name CA or name C or name O or name \ CB )) or resid 433)) selection = (chain 'C' and ((resid 126 through 136 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 139 and (name N or name CA or \ name C or name O or name CB )) or (resid 140 through 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 and (name N or name CA or name C or name O or name \ CB )) or resid 178 or (resid 179 through 207 and (name N or name CA or name C o \ r name O or name CB )) or resid 208 or (resid 209 through 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 24 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 244 or (resi \ d 245 through 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) o \ r resid 264 or (resid 265 and (name N or name CA or name C or name O or name CB \ )) or (resid 268 and (name N or name CA or name C or name O or name CB )) or res \ id 269 or (resid 270 through 273 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 274 through 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 or (resid 314 through 327 and (name N or name CA or na \ me C or name O or name CB )) or (resid 328 through 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (name \ N or name CA or name C or name O or name CB )) or resid 336 or (resid 337 throu \ gh 364 and (name N or name CA or name C or name O or name CB )) or (resid 371 th \ rough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 through 381 and (name N or name CA or name C or name O or name CB \ )) or (resid 382 through 432 and (name N or name CA or name C or name O or name \ CB )) or resid 433)) selection = (chain 'D' and ((resid 126 through 136 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 139 and (name N or name CA or \ name C or name O or name CB )) or (resid 140 through 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 and (name N or name CA or name C or name O or name \ CB )) or resid 178 or (resid 179 through 207 and (name N or name CA or name C o \ r name O or name CB )) or resid 208 or (resid 209 through 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 24 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 244 or (resi \ d 245 through 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) o \ r resid 264 or (resid 265 and (name N or name CA or name C or name O or name CB \ )) or (resid 268 and (name N or name CA or name C or name O or name CB )) or res \ id 269 or (resid 270 through 273 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 274 through 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 or (resid 314 through 327 and (name N or name CA or na \ me C or name O or name CB )) or (resid 328 through 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (name \ N or name CA or name C or name O or name CB )) or resid 336 or (resid 337 throu \ gh 364 and (name N or name CA or name C or name O or name CB )) or (resid 371 th \ rough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 through 381 and (name N or name CA or name C or name O or name CB \ )) or (resid 382 through 432 and (name N or name CA or name C or name O or name \ CB )) or resid 433)) selection = (chain 'E' and ((resid 126 through 136 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 139 and (name N or name CA or \ name C or name O or name CB )) or (resid 140 through 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 and (name N or name CA or name C or name O or name \ CB )) or resid 178 or (resid 179 through 207 and (name N or name CA or name C o \ r name O or name CB )) or resid 208 or (resid 209 through 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 24 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 244 or (resi \ d 245 through 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) o \ r resid 264 or (resid 265 and (name N or name CA or name C or name O or name CB \ )) or (resid 268 and (name N or name CA or name C or name O or name CB )) or res \ id 269 or (resid 270 through 273 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 274 through 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 or (resid 314 through 327 and (name N or name CA or na \ me C or name O or name CB )) or (resid 328 through 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (name \ N or name CA or name C or name O or name CB )) or resid 336 or (resid 337 throu \ gh 364 and (name N or name CA or name C or name O or name CB )) or (resid 371 th \ rough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 through 381 and (name N or name CA or name C or name O or name CB \ )) or (resid 382 through 432 and (name N or name CA or name C or name O or name \ CB )) or resid 433)) selection = (chain 'F' and resid 126 through 433) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = (chain 'S' and resid 290 through 330) } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 4.550 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 48.590 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.150 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 16882 Z= 0.495 Angle : 1.145 14.931 22990 Z= 0.754 Chirality : 0.072 0.367 2773 Planarity : 0.006 0.056 3027 Dihedral : 13.965 168.510 5645 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.09 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.14), residues: 2383 helix: -2.12 (0.11), residues: 1356 sheet: -2.00 (0.35), residues: 194 loop : -2.54 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 280 HIS 0.001 0.000 HIS E 157 PHE 0.012 0.001 PHE A 308 TYR 0.008 0.001 TYR C 181 ARG 0.002 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.188 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: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8551 (mt) cc_final: 0.8120 (tt) REVERT: A 307 MET cc_start: 0.8242 (ttm) cc_final: 0.7536 (tpp) REVERT: B 307 MET cc_start: 0.8205 (ttm) cc_final: 0.7469 (tpp) REVERT: C 341 VAL cc_start: 0.9106 (m) cc_final: 0.8865 (p) REVERT: C 386 MET cc_start: 0.7700 (ptp) cc_final: 0.7414 (ptt) REVERT: C 427 GLN cc_start: 0.7117 (tp40) cc_final: 0.6657 (tp-100) REVERT: C 431 ASP cc_start: 0.6501 (m-30) cc_final: 0.6032 (m-30) REVERT: D 145 LEU cc_start: 0.9248 (mt) cc_final: 0.9038 (mt) REVERT: D 186 VAL cc_start: 0.9402 (t) cc_final: 0.9175 (p) REVERT: D 386 MET cc_start: 0.6842 (ptp) cc_final: 0.6610 (ppp) REVERT: D 431 ASP cc_start: 0.7513 (m-30) cc_final: 0.6609 (m-30) REVERT: E 170 LEU cc_start: 0.8232 (tp) cc_final: 0.7999 (tt) REVERT: E 386 MET cc_start: 0.6916 (ptp) cc_final: 0.6594 (ptp) REVERT: E 418 ASN cc_start: 0.8800 (t0) cc_final: 0.8571 (m-40) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2922 time to fit residues: 88.7210 Evaluate side-chains 100 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN B 216 GLN B 277 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 437 ASN D 216 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 GLN E 311 ASN E 425 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16882 Z= 0.314 Angle : 0.712 7.939 22990 Z= 0.370 Chirality : 0.041 0.235 2773 Planarity : 0.005 0.058 3027 Dihedral : 8.792 138.296 2580 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2383 helix: 0.08 (0.14), residues: 1393 sheet: -1.27 (0.35), residues: 220 loop : -1.57 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 132 HIS 0.014 0.004 HIS A 359 PHE 0.019 0.002 PHE C 195 TYR 0.017 0.002 TYR B 334 ARG 0.007 0.001 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 2.148 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: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8982 (mt) cc_final: 0.8589 (tp) REVERT: A 307 MET cc_start: 0.8545 (ttm) cc_final: 0.8042 (ttm) REVERT: B 307 MET cc_start: 0.8455 (ttm) cc_final: 0.8130 (ttt) REVERT: C 386 MET cc_start: 0.8067 (ptp) cc_final: 0.7487 (ptp) REVERT: D 307 MET cc_start: 0.8498 (mtt) cc_final: 0.8289 (mmm) REVERT: D 386 MET cc_start: 0.7660 (ptp) cc_final: 0.7207 (ppp) REVERT: E 386 MET cc_start: 0.7179 (ptp) cc_final: 0.6779 (ptp) outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.2362 time to fit residues: 42.1617 Evaluate side-chains 83 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 181 optimal weight: 50.0000 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 235 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 281 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 ASN E 427 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 16882 Z= 0.330 Angle : 0.709 8.905 22990 Z= 0.367 Chirality : 0.042 0.222 2773 Planarity : 0.005 0.098 3027 Dihedral : 8.475 123.301 2580 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.15 % Allowed : 5.86 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2383 helix: 1.11 (0.14), residues: 1421 sheet: -1.08 (0.36), residues: 227 loop : -1.25 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 388 HIS 0.011 0.003 HIS A 359 PHE 0.047 0.003 PHE C 308 TYR 0.022 0.002 TYR C 181 ARG 0.010 0.001 ARG C 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8475 (ttm) cc_final: 0.7991 (ttm) REVERT: B 307 MET cc_start: 0.8217 (ttm) cc_final: 0.7975 (ttp) REVERT: C 170 LEU cc_start: 0.8455 (tp) cc_final: 0.8210 (tt) REVERT: C 386 MET cc_start: 0.8148 (ptp) cc_final: 0.7516 (ptp) outliers start: 2 outliers final: 0 residues processed: 85 average time/residue: 0.2365 time to fit residues: 34.2666 Evaluate side-chains 65 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 20.0000 chunk 164 optimal weight: 50.0000 chunk 113 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN B 437 ASN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN D 265 ASN D 355 GLN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16882 Z= 0.192 Angle : 0.568 9.962 22990 Z= 0.283 Chirality : 0.040 0.268 2773 Planarity : 0.004 0.050 3027 Dihedral : 7.910 117.334 2580 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.07 % Allowed : 2.45 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2383 helix: 1.79 (0.14), residues: 1412 sheet: -0.96 (0.35), residues: 222 loop : -0.91 (0.25), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 388 HIS 0.007 0.001 HIS A 359 PHE 0.021 0.002 PHE A 218 TYR 0.012 0.001 TYR A 181 ARG 0.005 0.001 ARG C 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.9185 (mt) cc_final: 0.8700 (tp) REVERT: A 307 MET cc_start: 0.8493 (ttm) cc_final: 0.7998 (ttm) REVERT: C 386 MET cc_start: 0.8134 (ptp) cc_final: 0.7491 (ptp) REVERT: D 170 LEU cc_start: 0.8164 (tp) cc_final: 0.7946 (tp) REVERT: D 307 MET cc_start: 0.8467 (mtt) cc_final: 0.8076 (mmm) REVERT: E 348 MET cc_start: 0.7511 (mmt) cc_final: 0.7109 (mmm) REVERT: E 386 MET cc_start: 0.7333 (ptp) cc_final: 0.7130 (ptp) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.2276 time to fit residues: 31.3799 Evaluate side-chains 63 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 40.0000 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 172 optimal weight: 50.0000 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 118 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.6856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 16882 Z= 0.336 Angle : 0.702 9.508 22990 Z= 0.362 Chirality : 0.041 0.211 2773 Planarity : 0.005 0.054 3027 Dihedral : 8.006 112.239 2580 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.96 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2383 helix: 1.64 (0.14), residues: 1416 sheet: -1.12 (0.35), residues: 226 loop : -0.94 (0.26), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 388 HIS 0.009 0.002 HIS D 157 PHE 0.024 0.003 PHE A 218 TYR 0.018 0.002 TYR A 324 ARG 0.010 0.001 ARG E 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.900 Fit side-chains REVERT: A 307 MET cc_start: 0.8453 (ttm) cc_final: 0.8077 (ttm) REVERT: C 386 MET cc_start: 0.8325 (ptp) cc_final: 0.7672 (ptp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2291 time to fit residues: 28.1956 Evaluate side-chains 55 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.0770 chunk 208 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN D 157 HIS ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.7254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16882 Z= 0.247 Angle : 0.608 10.171 22990 Z= 0.308 Chirality : 0.040 0.187 2773 Planarity : 0.004 0.042 3027 Dihedral : 7.699 112.771 2580 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.18), residues: 2383 helix: 1.91 (0.14), residues: 1412 sheet: -1.01 (0.35), residues: 231 loop : -0.83 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 388 HIS 0.008 0.002 HIS A 359 PHE 0.016 0.002 PHE D 159 TYR 0.014 0.002 TYR A 181 ARG 0.006 0.001 ARG C 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8403 (ttm) cc_final: 0.8004 (ttm) REVERT: C 386 MET cc_start: 0.8326 (ptp) cc_final: 0.7652 (ptp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2252 time to fit residues: 26.1261 Evaluate side-chains 56 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 132 optimal weight: 0.0770 chunk 169 optimal weight: 50.0000 chunk 131 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 129 optimal weight: 0.0670 chunk 231 optimal weight: 40.0000 chunk 144 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 3.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.7372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16882 Z= 0.177 Angle : 0.559 7.442 22990 Z= 0.278 Chirality : 0.040 0.178 2773 Planarity : 0.004 0.041 3027 Dihedral : 7.467 111.028 2580 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.19), residues: 2383 helix: 2.18 (0.14), residues: 1422 sheet: -0.71 (0.36), residues: 210 loop : -0.87 (0.25), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 388 HIS 0.007 0.001 HIS A 359 PHE 0.014 0.001 PHE D 159 TYR 0.013 0.001 TYR A 181 ARG 0.007 0.001 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.970 Fit side-chains REVERT: A 307 MET cc_start: 0.8420 (ttm) cc_final: 0.7990 (ttm) REVERT: C 386 MET cc_start: 0.8336 (ptp) cc_final: 0.7635 (ptp) REVERT: E 348 MET cc_start: 0.7670 (mmt) cc_final: 0.7306 (mmm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2129 time to fit residues: 25.3819 Evaluate side-chains 57 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 69 optimal weight: 0.1980 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 157 optimal weight: 50.0000 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 181 optimal weight: 40.0000 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.7965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 16882 Z= 0.271 Angle : 0.645 7.984 22990 Z= 0.327 Chirality : 0.041 0.308 2773 Planarity : 0.004 0.043 3027 Dihedral : 7.652 113.515 2580 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.18), residues: 2383 helix: 1.95 (0.14), residues: 1432 sheet: -1.09 (0.33), residues: 245 loop : -0.85 (0.26), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 388 HIS 0.008 0.002 HIS A 359 PHE 0.020 0.002 PHE E 230 TYR 0.013 0.002 TYR A 324 ARG 0.007 0.001 ARG C 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.373 Fit side-chains REVERT: A 220 MET cc_start: 0.8350 (ttm) cc_final: 0.8097 (ttm) REVERT: A 307 MET cc_start: 0.8509 (ttm) cc_final: 0.8115 (ttm) REVERT: B 307 MET cc_start: 0.8624 (mtp) cc_final: 0.7815 (tpp) REVERT: C 307 MET cc_start: 0.7795 (mmm) cc_final: 0.7314 (mmt) REVERT: C 386 MET cc_start: 0.8301 (ptp) cc_final: 0.7584 (ptp) REVERT: D 170 LEU cc_start: 0.8375 (tp) cc_final: 0.8096 (tt) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2268 time to fit residues: 25.9032 Evaluate side-chains 55 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 5.9990 chunk 221 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 50.0000 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 203 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.8204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16882 Z= 0.232 Angle : 0.594 7.160 22990 Z= 0.300 Chirality : 0.040 0.309 2773 Planarity : 0.004 0.040 3027 Dihedral : 7.530 124.886 2580 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.19), residues: 2383 helix: 2.11 (0.14), residues: 1425 sheet: -0.99 (0.34), residues: 240 loop : -0.79 (0.26), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 388 HIS 0.007 0.001 HIS A 359 PHE 0.015 0.002 PHE E 230 TYR 0.014 0.001 TYR A 181 ARG 0.012 0.001 ARG D 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 2.150 Fit side-chains revert: symmetry clash REVERT: A 220 MET cc_start: 0.8296 (ttm) cc_final: 0.8051 (ttm) REVERT: A 307 MET cc_start: 0.8503 (ttm) cc_final: 0.8154 (ttm) REVERT: D 170 LEU cc_start: 0.8424 (tp) cc_final: 0.8202 (tt) REVERT: D 260 MET cc_start: 0.8231 (ppp) cc_final: 0.7629 (ppp) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.2551 time to fit residues: 28.9029 Evaluate side-chains 56 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 158 optimal weight: 40.0000 chunk 239 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 chunk 190 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 147 optimal weight: 0.0970 chunk 116 optimal weight: 8.9990 overall best weight: 4.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.8453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16882 Z= 0.227 Angle : 0.596 7.607 22990 Z= 0.300 Chirality : 0.040 0.264 2773 Planarity : 0.004 0.042 3027 Dihedral : 7.522 129.240 2580 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.19), residues: 2383 helix: 2.16 (0.14), residues: 1420 sheet: -0.94 (0.34), residues: 239 loop : -0.77 (0.26), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 388 HIS 0.007 0.001 HIS A 359 PHE 0.016 0.002 PHE E 230 TYR 0.013 0.001 TYR A 181 ARG 0.006 0.001 ARG E 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.785 Fit side-chains REVERT: A 220 MET cc_start: 0.8277 (ttm) cc_final: 0.8055 (ttm) REVERT: C 307 MET cc_start: 0.7863 (mmm) cc_final: 0.7251 (mmt) REVERT: C 330 MET cc_start: 0.8022 (mpp) cc_final: 0.6960 (tpp) REVERT: D 170 LEU cc_start: 0.8430 (tp) cc_final: 0.8178 (tt) REVERT: E 348 MET cc_start: 0.7286 (mmp) cc_final: 0.7029 (mmm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2164 time to fit residues: 25.7112 Evaluate side-chains 57 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 175 optimal weight: 30.0000 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 0.0470 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.037354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.028595 restraints weight = 197462.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.029247 restraints weight = 133105.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.029674 restraints weight = 99510.852| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.8333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16882 Z= 0.126 Angle : 0.550 7.733 22990 Z= 0.265 Chirality : 0.040 0.250 2773 Planarity : 0.003 0.039 3027 Dihedral : 7.144 125.987 2580 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2383 helix: 2.48 (0.14), residues: 1413 sheet: -0.72 (0.34), residues: 235 loop : -0.59 (0.26), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 206 HIS 0.005 0.001 HIS A 359 PHE 0.011 0.001 PHE E 290 TYR 0.010 0.001 TYR A 181 ARG 0.010 0.000 ARG B 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2289.07 seconds wall clock time: 43 minutes 10.67 seconds (2590.67 seconds total)