Starting phenix.real_space_refine on Thu Feb 15 22:55:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kuy_23041/02_2024/7kuy_23041_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kuy_23041/02_2024/7kuy_23041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kuy_23041/02_2024/7kuy_23041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kuy_23041/02_2024/7kuy_23041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kuy_23041/02_2024/7kuy_23041_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kuy_23041/02_2024/7kuy_23041_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 83 5.16 5 C 8906 2.51 5 N 2177 2.21 5 O 2467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A ASP 93": "OD1" <-> "OD2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ASP 32": "OD1" <-> "OD2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 148": "OD1" <-> "OD2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 291": "OD1" <-> "OD2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ASP 91": "OD1" <-> "OD2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ASP 291": "OD1" <-> "OD2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 133": "OD1" <-> "OD2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E ASP 210": "OD1" <-> "OD2" Residue "E ASP 215": "OD1" <-> "OD2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 456": "NH1" <-> "NH2" Residue "E PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13633 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2698 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2697 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2674 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2663 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "E" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2650 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.59, per 1000 atoms: 0.56 Number of scatterers: 13633 At special positions: 0 Unit cell: (91.3, 91.3, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 83 16.00 O 2467 8.00 N 2177 7.00 C 8906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 216 " distance=2.04 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 45 " " NAG A 502 " - " ASN A 76 " " NAG B 501 " - " ASN B 45 " " NAG B 502 " - " ASN B 76 " " NAG C 501 " - " ASN C 45 " " NAG C 502 " - " ASN C 76 " " NAG D 501 " - " ASN D 45 " " NAG D 502 " - " ASN D 76 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 2.6 seconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 19 sheets defined 32.2% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 4.194A pdb=" N ASP A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 236 through 250 removed outlier: 3.843A pdb=" N PHE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 280 Processing helix chain 'A' and resid 289 through 314 removed outlier: 3.814A pdb=" N TRP A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 297 " --> pdb=" O TRP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 415 Proline residue: A 400 - end of helix Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 235 through 250 removed outlier: 3.691A pdb=" N PHE B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 removed outlier: 4.225A pdb=" N ARG B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 315 removed outlier: 3.517A pdb=" N CYS B 297 " --> pdb=" O TRP B 293 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 298 " --> pdb=" O MET B 294 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 413 removed outlier: 4.170A pdb=" N ALA B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Proline residue: B 400 - end of helix removed outlier: 3.800A pdb=" N PHE B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 25 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 236 through 251 removed outlier: 4.217A pdb=" N PHE C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE C 251 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 275 removed outlier: 3.848A pdb=" N ALA C 261 " --> pdb=" O PRO C 257 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 315 Processing helix chain 'C' and resid 385 through 415 Proline residue: C 400 - end of helix removed outlier: 3.982A pdb=" N THR C 413 " --> pdb=" O PHE C 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 235 through 250 removed outlier: 3.802A pdb=" N PHE D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 279 removed outlier: 4.073A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 313 removed outlier: 3.594A pdb=" N TRP D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU D 298 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 408 removed outlier: 4.108A pdb=" N ILE D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Proline residue: D 400 - end of helix Processing helix chain 'E' and resid 33 through 36 No H-bonds generated for 'chain 'E' and resid 33 through 36' Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 165 through 170 removed outlier: 3.536A pdb=" N PHE E 168 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Proline residue: E 169 - end of helix No H-bonds generated for 'chain 'E' and resid 165 through 170' Processing helix chain 'E' and resid 245 through 248 No H-bonds generated for 'chain 'E' and resid 245 through 248' Processing helix chain 'E' and resid 253 through 267 removed outlier: 4.406A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 281 Processing helix chain 'E' and resid 283 through 297 removed outlier: 4.002A pdb=" N THR E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 328 Processing helix chain 'E' and resid 452 through 473 removed outlier: 3.860A pdb=" N ALA E 457 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 460 - end of helix removed outlier: 4.347A pdb=" N LEU E 464 " --> pdb=" O PRO E 460 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE E 465 " --> pdb=" O PHE E 461 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE E 466 " --> pdb=" O CYS E 462 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP E 471 " --> pdb=" O ASN E 467 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 173 through 177 removed outlier: 6.187A pdb=" N VAL A 44 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLU A 176 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 46 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN A 68 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE A 55 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG A 66 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU A 125 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 removed outlier: 3.815A pdb=" N GLN A 184 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 160 through 164 removed outlier: 4.070A pdb=" N CYS A 216 " --> pdb=" O CYS A 205 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 194 through 196 removed outlier: 3.576A pdb=" N GLU A 224 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 173 through 177 removed outlier: 5.870A pdb=" N VAL B 44 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU B 176 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 46 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 45 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ASN B 76 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B 68 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE B 55 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG B 66 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU B 125 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 92 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 105 through 107 Processing sheet with id= G, first strand: chain 'B' and resid 201 through 203 Processing sheet with id= H, first strand: chain 'B' and resid 207 through 209 removed outlier: 3.711A pdb=" N GLY B 212 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 173 through 177 removed outlier: 6.098A pdb=" N VAL C 44 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU C 176 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL C 46 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN C 45 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASN C 76 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C 68 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE C 55 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 66 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY C 112 " --> pdb=" O THR C 142 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 50 through 52 removed outlier: 3.775A pdb=" N GLN C 184 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.414A pdb=" N LEU C 125 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 105 through 107 Processing sheet with id= M, first strand: chain 'C' and resid 201 through 204 Processing sheet with id= N, first strand: chain 'D' and resid 173 through 177 removed outlier: 6.182A pdb=" N VAL D 44 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLU D 176 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL D 46 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN D 45 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN D 76 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN D 68 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE D 55 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG D 66 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU D 125 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 105 through 107 Processing sheet with id= P, first strand: chain 'D' and resid 110 through 114 removed outlier: 6.580A pdb=" N THR D 142 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA D 113 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR D 140 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 189 through 193 removed outlier: 6.166A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 86 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASP E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU E 141 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 108 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 68 through 70 removed outlier: 3.639A pdb=" N SER E 68 " --> pdb=" O ASN E 82 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 121 through 123 544 hydrogen bonds defined for protein. 1593 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: 4.06 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3300 1.33 - 1.45: 3147 1.45 - 1.58: 7421 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 14003 Sorted by residual: bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C ALA D 256 " pdb=" N PRO D 257 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.36e-02 5.41e+03 9.82e+00 bond pdb=" CAG SY9 D 503 " pdb=" CAV SY9 D 503 " ideal model delta sigma weight residual 1.578 1.522 0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" N ILE E 268 " pdb=" CA ILE E 268 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.32e-02 5.74e+03 7.73e+00 bond pdb=" N THR D 265 " pdb=" CA THR D 265 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.77e+00 ... (remaining 13998 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.75: 359 105.75 - 112.90: 7454 112.90 - 120.05: 5031 120.05 - 127.20: 6062 127.20 - 134.35: 195 Bond angle restraints: 19101 Sorted by residual: angle pdb=" N VAL E 330 " pdb=" CA VAL E 330 " pdb=" C VAL E 330 " ideal model delta sigma weight residual 113.53 108.56 4.97 9.80e-01 1.04e+00 2.58e+01 angle pdb=" C THR B 119 " pdb=" N THR B 120 " pdb=" CA THR B 120 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C GLN D 193 " pdb=" N PHE D 194 " pdb=" CA PHE D 194 " ideal model delta sigma weight residual 121.54 129.44 -7.90 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C VAL B 118 " pdb=" N THR B 119 " pdb=" CA THR B 119 " ideal model delta sigma weight residual 121.54 129.32 -7.78 1.91e+00 2.74e-01 1.66e+01 angle pdb=" C ASN E 39 " pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta sigma weight residual 121.54 129.32 -7.78 1.91e+00 2.74e-01 1.66e+01 ... (remaining 19096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.18: 8051 22.18 - 44.36: 496 44.36 - 66.54: 71 66.54 - 88.72: 14 88.72 - 110.90: 3 Dihedral angle restraints: 8635 sinusoidal: 3626 harmonic: 5009 Sorted by residual: dihedral pdb=" CA LEU E 167 " pdb=" C LEU E 167 " pdb=" N PHE E 168 " pdb=" CA PHE E 168 " ideal model delta harmonic sigma weight residual 180.00 -154.79 -25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASN B 151 " pdb=" C ASN B 151 " pdb=" N PHE B 152 " pdb=" CA PHE B 152 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ILE A 69 " pdb=" C ILE A 69 " pdb=" N PHE A 70 " pdb=" CA PHE A 70 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 8632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1982 0.090 - 0.179: 196 0.179 - 0.269: 20 0.269 - 0.358: 11 0.358 - 0.448: 6 Chirality restraints: 2215 Sorted by residual: chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 76 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" NAY SY9 E 502 " pdb=" CAS SY9 E 502 " pdb=" CAV SY9 E 502 " pdb=" CAX SY9 E 502 " both_signs ideal model delta sigma weight residual False -2.12 -2.52 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" NAY SY9 D 503 " pdb=" CAS SY9 D 503 " pdb=" CAV SY9 D 503 " pdb=" CAX SY9 D 503 " both_signs ideal model delta sigma weight residual False -2.12 -2.51 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 2212 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAA SY9 C 503 " -0.121 2.00e-02 2.50e+03 9.70e-02 1.41e+02 pdb=" CAI SY9 C 503 " 0.037 2.00e-02 2.50e+03 pdb=" CAK SY9 C 503 " -0.016 2.00e-02 2.50e+03 pdb=" CAL SY9 C 503 " -0.082 2.00e-02 2.50e+03 pdb=" NAH SY9 C 503 " 0.183 2.00e-02 2.50e+03 pdb=" OAJ SY9 C 503 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 253 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO E 254 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 254 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 254 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 118 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C VAL A 118 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 118 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 119 " 0.013 2.00e-02 2.50e+03 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1621 2.75 - 3.28: 12912 3.28 - 3.82: 22102 3.82 - 4.36: 25846 4.36 - 4.90: 45631 Nonbonded interactions: 108112 Sorted by model distance: nonbonded pdb=" OG1 THR B 62 " pdb=" OD2 ASP B 64 " model vdw 2.208 2.440 nonbonded pdb=" OG SER D 285 " pdb=" O GLN E 243 " model vdw 2.218 2.440 nonbonded pdb=" O LEU D 105 " pdb=" OG1 THR E 135 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR E 185 " pdb=" OD1 ASP E 187 " model vdw 2.225 2.440 nonbonded pdb=" OG SER C 285 " pdb=" O GLN D 226 " model vdw 2.235 2.440 ... (remaining 108107 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 15 through 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB )) or resid 20 through 21 or (resid 22 and (name N or nam \ e CA or name C or name O or name CB )) or resid 23 through 33 or (resid 34 and ( \ name N or name CA or name C or name O or name CB )) or resid 35 through 59 or (r \ esid 60 and (name N or name CA or name C or name O or name CB )) or resid 61 thr \ ough 175 or (resid 176 and (name N or name CA or name C or name O or name CB )) \ or resid 177 through 186 or (resid 187 and (name N or name CA or name C or name \ O or name CB )) or resid 188 through 250 or (resid 251 and (name N or name CA or \ name C or name O or name CB )) or resid 252 through 253 or (resid 254 through 2 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 257 through \ 305 or (resid 306 and (name N or name CA or name C or name O or name CB )) or r \ esid 307 through 315 or (resid 316 through 398 and (name N or name CA or name C \ or name O or name CB )) or resid 399 through 400 or (resid 401 through 402 and ( \ name N or name CA or name C or name O or name CB )) or resid 403 through 408 or \ (resid 409 and (name N or name CA or name C or name O or name CB )) or resid 410 \ through 419 or resid 501 through 503)) selection = (chain 'B' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 18 or (resid 19 and (name N or name CA or name C or name \ O or name CB )) or resid 20 through 21 or (resid 22 and (name N or name CA or na \ me C or name O or name CB )) or resid 23 through 33 or (resid 34 and (name N or \ name CA or name C or name O or name CB )) or resid 35 through 175 or (resid 176 \ and (name N or name CA or name C or name O or name CB )) or resid 177 through 18 \ 6 or (resid 187 and (name N or name CA or name C or name O or name CB )) or resi \ d 188 through 250 or (resid 251 and (name N or name CA or name C or name O or na \ me CB )) or resid 252 through 305 or (resid 306 and (name N or name CA or name C \ or name O or name CB )) or resid 307 through 315 or (resid 316 through 398 and \ (name N or name CA or name C or name O or name CB )) or resid 399 through 400 or \ (resid 401 through 402 and (name N or name CA or name C or name O or name CB )) \ or resid 403 through 404 or (resid 405 and (name N or name CA or name C or name \ O or name CB )) or resid 406 through 408 or (resid 409 and (name N or name CA o \ r name C or name O or name CB )) or resid 410 through 419 or resid 501 through 5 \ 03)) selection = (chain 'C' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 21 or (resid 22 and (name N or name CA or name C or name \ O or name CB )) or resid 23 through 59 or (resid 60 and (name N or name CA or na \ me C or name O or name CB )) or resid 61 through 175 or (resid 176 and (name N o \ r name CA or name C or name O or name CB )) or resid 177 through 186 or (resid 1 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 188 through \ 305 or (resid 306 and (name N or name CA or name C or name O or name CB )) or r \ esid 307 through 386 or (resid 387 through 398 and (name N or name CA or name C \ or name O or name CB )) or resid 399 through 404 or (resid 405 and (name N or na \ me CA or name C or name O or name CB )) or resid 406 through 419 or resid 501 th \ rough 503)) selection = (chain 'D' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 59 or (resid 60 and (name N or name CA or name C or name \ O or name CB )) or resid 61 through 250 or (resid 251 and (name N or name CA or \ name C or name O or name CB )) or resid 252 or (resid 253 through 256 and (name \ N or name CA or name C or name O or name CB )) or resid 257 through 400 or (resi \ d 401 through 402 and (name N or name CA or name C or name O or name CB )) or re \ sid 403 through 404 or (resid 405 and (name N or name CA or name C or name O or \ name CB )) or resid 406 through 408 or (resid 409 and (name N or name CA or name \ C or name O or name CB )) or resid 410 through 419 or resid 501 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.390 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 38.960 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 14003 Z= 0.396 Angle : 0.914 10.877 19101 Z= 0.475 Chirality : 0.062 0.448 2215 Planarity : 0.006 0.097 2352 Dihedral : 14.527 110.898 5367 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.14 % Allowed : 11.59 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.17), residues: 1674 helix: -1.88 (0.17), residues: 571 sheet: -2.83 (0.23), residues: 390 loop : -3.52 (0.18), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 293 HIS 0.003 0.001 HIS E 132 PHE 0.020 0.002 PHE E 69 TYR 0.020 0.002 TYR C 135 ARG 0.005 0.000 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 262 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7773 (mtm) cc_final: 0.7078 (mpp) REVERT: B 63 MET cc_start: 0.8910 (mmt) cc_final: 0.8569 (mmt) REVERT: B 172 ASP cc_start: 0.7617 (m-30) cc_final: 0.7307 (m-30) REVERT: B 217 ILE cc_start: 0.9236 (pt) cc_final: 0.8960 (pt) REVERT: C 25 MET cc_start: 0.8487 (ptp) cc_final: 0.8248 (ptp) REVERT: C 82 TYR cc_start: 0.8154 (p90) cc_final: 0.7787 (p90) REVERT: C 197 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7851 (mmtt) REVERT: C 224 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7645 (tm-30) REVERT: C 407 ASN cc_start: 0.8430 (t0) cc_final: 0.8135 (t0) REVERT: E 180 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7638 (mt-10) REVERT: E 223 LYS cc_start: 0.8657 (mmtp) cc_final: 0.8451 (mttm) REVERT: E 235 GLU cc_start: 0.8259 (pt0) cc_final: 0.7872 (pt0) outliers start: 2 outliers final: 1 residues processed: 264 average time/residue: 0.2462 time to fit residues: 95.6246 Evaluate side-chains 196 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 129 optimal weight: 30.0000 chunk 50 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 149 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN D 74 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14003 Z= 0.157 Angle : 0.610 9.736 19101 Z= 0.301 Chirality : 0.044 0.332 2215 Planarity : 0.004 0.058 2352 Dihedral : 8.194 99.946 2336 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.29 % Allowed : 17.00 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.19), residues: 1674 helix: -0.31 (0.21), residues: 562 sheet: -2.32 (0.24), residues: 389 loop : -3.11 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 246 HIS 0.002 0.000 HIS D 222 PHE 0.016 0.001 PHE D 249 TYR 0.016 0.001 TYR E 303 ARG 0.008 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 222 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8175 (t0) cc_final: 0.7925 (t0) REVERT: A 154 MET cc_start: 0.7669 (mtm) cc_final: 0.6853 (mpp) REVERT: B 63 MET cc_start: 0.8902 (mmt) cc_final: 0.8640 (mmt) REVERT: B 172 ASP cc_start: 0.7579 (m-30) cc_final: 0.7262 (m-30) REVERT: C 22 ASP cc_start: 0.8465 (m-30) cc_final: 0.7668 (t0) REVERT: C 82 TYR cc_start: 0.8166 (p90) cc_final: 0.7788 (p90) REVERT: C 197 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7690 (mmtt) REVERT: C 224 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7562 (tm-30) REVERT: D 138 ARG cc_start: 0.9009 (ttt-90) cc_final: 0.8591 (ttt-90) REVERT: E 116 LEU cc_start: 0.8926 (pp) cc_final: 0.8712 (pp) REVERT: E 197 ASP cc_start: 0.6410 (p0) cc_final: 0.6137 (p0) REVERT: E 235 GLU cc_start: 0.8218 (pt0) cc_final: 0.7753 (pt0) outliers start: 33 outliers final: 20 residues processed: 244 average time/residue: 0.2583 time to fit residues: 93.9321 Evaluate side-chains 223 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 158 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 14003 Z= 0.464 Angle : 0.699 9.850 19101 Z= 0.352 Chirality : 0.048 0.339 2215 Planarity : 0.004 0.066 2352 Dihedral : 7.916 93.946 2336 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.82 % Allowed : 19.99 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.20), residues: 1674 helix: 0.18 (0.22), residues: 558 sheet: -2.30 (0.24), residues: 392 loop : -3.03 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 246 HIS 0.002 0.001 HIS E 132 PHE 0.016 0.002 PHE E 69 TYR 0.018 0.002 TYR B 229 ARG 0.010 0.001 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 196 time to evaluate : 1.726 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8307 (t0) cc_final: 0.8083 (t0) REVERT: B 63 MET cc_start: 0.8903 (mmt) cc_final: 0.8611 (mmt) REVERT: B 233 GLN cc_start: 0.8128 (mm110) cc_final: 0.7838 (mm-40) REVERT: C 197 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7847 (mmtt) REVERT: C 224 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7668 (tm-30) REVERT: E 180 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7847 (mt-10) REVERT: E 235 GLU cc_start: 0.8273 (pt0) cc_final: 0.8003 (pt0) REVERT: E 244 VAL cc_start: 0.8900 (m) cc_final: 0.8526 (t) outliers start: 55 outliers final: 37 residues processed: 237 average time/residue: 0.2254 time to fit residues: 80.7042 Evaluate side-chains 219 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 233 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14003 Z= 0.179 Angle : 0.589 9.889 19101 Z= 0.292 Chirality : 0.044 0.353 2215 Planarity : 0.004 0.057 2352 Dihedral : 7.373 92.403 2336 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.02 % Allowed : 22.28 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.20), residues: 1674 helix: 0.68 (0.22), residues: 559 sheet: -1.95 (0.25), residues: 402 loop : -2.76 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP D 246 HIS 0.001 0.000 HIS D 116 PHE 0.016 0.001 PHE C 302 TYR 0.015 0.001 TYR E 303 ARG 0.006 0.000 ARG E 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 196 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8308 (t0) cc_final: 0.7975 (t0) REVERT: A 154 MET cc_start: 0.7463 (mtm) cc_final: 0.7255 (mpp) REVERT: A 273 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: B 63 MET cc_start: 0.8865 (mmt) cc_final: 0.8633 (mmt) REVERT: B 233 GLN cc_start: 0.8006 (mm110) cc_final: 0.7771 (mm-40) REVERT: C 22 ASP cc_start: 0.8446 (m-30) cc_final: 0.7764 (t0) REVERT: C 197 LYS cc_start: 0.7934 (mmmt) cc_final: 0.7649 (mmtt) REVERT: C 224 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7592 (tm-30) REVERT: E 116 LEU cc_start: 0.8970 (pp) cc_final: 0.8749 (pp) REVERT: E 180 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7295 (mt-10) REVERT: E 235 GLU cc_start: 0.8238 (pt0) cc_final: 0.7757 (pt0) REVERT: E 244 VAL cc_start: 0.8674 (m) cc_final: 0.8417 (t) outliers start: 58 outliers final: 32 residues processed: 242 average time/residue: 0.2278 time to fit residues: 83.5747 Evaluate side-chains 220 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 292 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 0.0060 chunk 118 optimal weight: 0.0470 chunk 65 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.0980 chunk 143 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14003 Z= 0.138 Angle : 0.578 10.464 19101 Z= 0.283 Chirality : 0.043 0.330 2215 Planarity : 0.003 0.052 2352 Dihedral : 6.763 87.848 2332 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.75 % Allowed : 23.18 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.21), residues: 1674 helix: 0.92 (0.23), residues: 561 sheet: -1.52 (0.27), residues: 385 loop : -2.56 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP D 246 HIS 0.001 0.000 HIS D 116 PHE 0.023 0.001 PHE C 249 TYR 0.017 0.001 TYR E 470 ARG 0.006 0.000 ARG E 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 207 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8271 (t0) cc_final: 0.7905 (t0) REVERT: B 63 MET cc_start: 0.8837 (mmt) cc_final: 0.8626 (mmt) REVERT: B 233 GLN cc_start: 0.7842 (mm110) cc_final: 0.7485 (mm110) REVERT: C 22 ASP cc_start: 0.8415 (m-30) cc_final: 0.7738 (t0) REVERT: C 197 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7589 (mmtt) REVERT: C 224 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7497 (tm-30) REVERT: E 113 TYR cc_start: 0.8540 (t80) cc_final: 0.7858 (t80) REVERT: E 116 LEU cc_start: 0.8896 (pp) cc_final: 0.8686 (pp) REVERT: E 177 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8186 (ptp) REVERT: E 235 GLU cc_start: 0.8225 (pt0) cc_final: 0.7769 (pt0) REVERT: E 244 VAL cc_start: 0.8471 (m) cc_final: 0.8257 (t) outliers start: 54 outliers final: 32 residues processed: 248 average time/residue: 0.2093 time to fit residues: 80.5233 Evaluate side-chains 233 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 292 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 159 optimal weight: 0.0570 chunk 132 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14003 Z= 0.180 Angle : 0.582 11.502 19101 Z= 0.284 Chirality : 0.044 0.342 2215 Planarity : 0.003 0.053 2352 Dihedral : 6.472 75.735 2332 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.30 % Allowed : 23.32 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1674 helix: 1.02 (0.23), residues: 561 sheet: -1.43 (0.27), residues: 394 loop : -2.50 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP D 246 HIS 0.001 0.000 HIS E 132 PHE 0.021 0.001 PHE C 249 TYR 0.015 0.001 TYR E 303 ARG 0.004 0.000 ARG E 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 210 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8320 (t0) cc_final: 0.7928 (t0) REVERT: A 278 ARG cc_start: 0.6298 (tpp80) cc_final: 0.5914 (tpp80) REVERT: C 22 ASP cc_start: 0.8444 (m-30) cc_final: 0.7786 (t0) REVERT: C 197 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7584 (mmtt) REVERT: C 224 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7503 (tm-30) REVERT: C 233 GLN cc_start: 0.7435 (tt0) cc_final: 0.7174 (tt0) REVERT: E 113 TYR cc_start: 0.8553 (t80) cc_final: 0.7856 (t80) REVERT: E 197 ASP cc_start: 0.6317 (p0) cc_final: 0.5978 (p0) REVERT: E 235 GLU cc_start: 0.8220 (pt0) cc_final: 0.7554 (pt0) REVERT: E 244 VAL cc_start: 0.8468 (m) cc_final: 0.8257 (t) outliers start: 62 outliers final: 40 residues processed: 258 average time/residue: 0.2107 time to fit residues: 83.4228 Evaluate side-chains 244 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 204 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 292 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 116 optimal weight: 0.0060 chunk 134 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14003 Z= 0.196 Angle : 0.595 11.252 19101 Z= 0.290 Chirality : 0.044 0.352 2215 Planarity : 0.003 0.053 2352 Dihedral : 6.116 59.522 2332 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.96 % Allowed : 24.64 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.21), residues: 1674 helix: 1.14 (0.23), residues: 561 sheet: -1.32 (0.27), residues: 394 loop : -2.42 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D 246 HIS 0.001 0.000 HIS E 132 PHE 0.028 0.001 PHE A 249 TYR 0.015 0.001 TYR E 303 ARG 0.006 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 213 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8319 (t0) cc_final: 0.7915 (t0) REVERT: C 22 ASP cc_start: 0.8415 (m-30) cc_final: 0.7760 (t0) REVERT: C 176 GLU cc_start: 0.7998 (pt0) cc_final: 0.7752 (mt-10) REVERT: C 197 LYS cc_start: 0.7943 (mmmt) cc_final: 0.7621 (mmtt) REVERT: C 224 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7490 (tm-30) REVERT: E 113 TYR cc_start: 0.8530 (t80) cc_final: 0.8107 (t80) REVERT: E 235 GLU cc_start: 0.8229 (pt0) cc_final: 0.7569 (pt0) REVERT: E 244 VAL cc_start: 0.8587 (m) cc_final: 0.8305 (t) outliers start: 57 outliers final: 44 residues processed: 256 average time/residue: 0.2162 time to fit residues: 85.1575 Evaluate side-chains 232 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 188 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 292 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14003 Z= 0.260 Angle : 0.615 9.766 19101 Z= 0.305 Chirality : 0.045 0.333 2215 Planarity : 0.004 0.055 2352 Dihedral : 6.128 59.689 2332 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.16 % Allowed : 24.50 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.21), residues: 1674 helix: 1.11 (0.23), residues: 561 sheet: -1.30 (0.27), residues: 394 loop : -2.38 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 246 HIS 0.002 0.000 HIS D 419 PHE 0.024 0.001 PHE A 249 TYR 0.015 0.001 TYR E 303 ARG 0.006 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 204 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8330 (t0) cc_final: 0.7943 (t0) REVERT: C 170 MET cc_start: 0.8551 (mmt) cc_final: 0.8322 (mmt) REVERT: C 176 GLU cc_start: 0.8032 (pt0) cc_final: 0.7784 (mt-10) REVERT: C 197 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7604 (mmtt) REVERT: C 224 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7532 (tm-30) REVERT: E 113 TYR cc_start: 0.8572 (t80) cc_final: 0.8096 (t80) REVERT: E 235 GLU cc_start: 0.8236 (pt0) cc_final: 0.7570 (pt0) REVERT: E 244 VAL cc_start: 0.8719 (m) cc_final: 0.8419 (t) outliers start: 60 outliers final: 51 residues processed: 250 average time/residue: 0.2177 time to fit residues: 83.2416 Evaluate side-chains 241 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 190 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14003 Z= 0.298 Angle : 0.641 10.029 19101 Z= 0.319 Chirality : 0.046 0.308 2215 Planarity : 0.004 0.055 2352 Dihedral : 6.113 59.026 2332 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.51 % Allowed : 24.91 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.21), residues: 1674 helix: 1.04 (0.23), residues: 557 sheet: -1.32 (0.27), residues: 394 loop : -2.34 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 246 HIS 0.002 0.000 HIS D 419 PHE 0.023 0.002 PHE A 249 TYR 0.017 0.001 TYR B 308 ARG 0.011 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 194 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8355 (t0) cc_final: 0.7978 (t0) REVERT: C 197 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7739 (mmtt) REVERT: C 224 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7617 (tm-30) REVERT: E 113 TYR cc_start: 0.8605 (t80) cc_final: 0.8165 (t80) REVERT: E 235 GLU cc_start: 0.8252 (pt0) cc_final: 0.7572 (pt0) REVERT: E 244 VAL cc_start: 0.8821 (m) cc_final: 0.8501 (t) outliers start: 65 outliers final: 53 residues processed: 241 average time/residue: 0.2211 time to fit residues: 83.1423 Evaluate side-chains 240 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 187 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 151 optimal weight: 0.0970 chunk 130 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14003 Z= 0.172 Angle : 0.606 9.747 19101 Z= 0.299 Chirality : 0.044 0.299 2215 Planarity : 0.003 0.054 2352 Dihedral : 5.859 59.537 2332 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.68 % Allowed : 25.82 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1674 helix: 1.21 (0.23), residues: 561 sheet: -1.20 (0.27), residues: 394 loop : -2.22 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 246 HIS 0.001 0.000 HIS D 116 PHE 0.024 0.001 PHE A 249 TYR 0.015 0.001 TYR B 308 ARG 0.013 0.000 ARG B 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 211 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8301 (t0) cc_final: 0.7890 (t0) REVERT: C 22 ASP cc_start: 0.8342 (m-30) cc_final: 0.7713 (t0) REVERT: C 176 GLU cc_start: 0.7995 (pt0) cc_final: 0.7762 (mt-10) REVERT: C 197 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7696 (mmtt) REVERT: C 224 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7559 (tm-30) REVERT: D 157 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8372 (mm110) REVERT: E 113 TYR cc_start: 0.8532 (t80) cc_final: 0.8078 (t80) REVERT: E 235 GLU cc_start: 0.8194 (pt0) cc_final: 0.7668 (pt0) REVERT: E 244 VAL cc_start: 0.8599 (m) cc_final: 0.8325 (t) REVERT: E 291 CYS cc_start: 0.7964 (m) cc_final: 0.7559 (m) outliers start: 53 outliers final: 45 residues processed: 252 average time/residue: 0.2125 time to fit residues: 82.2938 Evaluate side-chains 241 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 196 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 19 optimal weight: 0.0670 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.100337 restraints weight = 21440.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103700 restraints weight = 11039.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.105736 restraints weight = 7295.716| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14003 Z= 0.249 Angle : 0.625 9.775 19101 Z= 0.310 Chirality : 0.045 0.293 2215 Planarity : 0.004 0.055 2352 Dihedral : 5.862 59.709 2332 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.47 % Allowed : 26.51 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1674 helix: 1.22 (0.23), residues: 561 sheet: -1.19 (0.27), residues: 394 loop : -2.20 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 246 HIS 0.002 0.000 HIS D 419 PHE 0.022 0.002 PHE A 249 TYR 0.015 0.001 TYR E 303 ARG 0.013 0.000 ARG B 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.92 seconds wall clock time: 49 minutes 10.88 seconds (2950.88 seconds total)