Starting phenix.real_space_refine on Sun Dec 10 06:09:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l31_23148/12_2023/7l31_23148_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l31_23148/12_2023/7l31_23148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l31_23148/12_2023/7l31_23148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l31_23148/12_2023/7l31_23148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l31_23148/12_2023/7l31_23148_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l31_23148/12_2023/7l31_23148_updated.pdb" } resolution = 3.8 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 8883 2.51 5 N 2170 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ASP 32": "OD1" <-> "OD2" 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 ASP 64": "OD1" <-> "OD2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 180": "OD1" <-> "OD2" Residue "A GLU 201": "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 PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 117": "OD1" <-> "OD2" 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 PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 79": "NH1" <-> "NH2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 91": "OD1" <-> "OD2" Residue "D ASP 93": "OD1" <-> "OD2" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 99": "OD1" <-> "OD2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 210": "OD1" <-> "OD2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E ARG 456": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13596 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: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2613 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 78 Unusual residues: {'NAG': 2, 'SY9': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 7.30, per 1000 atoms: 0.54 Number of scatterers: 13596 At special positions: 0 Unit cell: (91.3, 90.47, 128.65, 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 2460 8.00 N 2170 7.00 C 8883 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=2.03 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: 5.47 Conformation dependent library (CDL) restraints added in 2.5 seconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 19 sheets defined 31.6% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.811A 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 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.705A pdb=" N PHE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 280 Processing helix chain 'A' and resid 291 through 314 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 228 through 233 Processing helix chain 'B' and resid 236 through 250 removed outlier: 3.828A pdb=" N PHE B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 278 removed outlier: 4.498A pdb=" N ARG B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 314 removed outlier: 4.032A pdb=" N VAL B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 415 removed outlier: 3.585A pdb=" N ALA B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Proline residue: B 400 - end of helix removed outlier: 3.609A pdb=" N PHE B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 25 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 235 through 250 removed outlier: 3.874A pdb=" N PHE C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 275 Processing helix chain 'C' and resid 289 through 315 Processing helix chain 'C' and resid 385 through 411 Proline residue: C 400 - end of helix 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: 3.874A pdb=" N PHE D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 278 Processing helix chain 'D' and resid 289 through 314 removed outlier: 3.849A pdb=" N TRP D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 298 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 414 Proline residue: D 400 - end of helix removed outlier: 4.163A pdb=" N THR D 413 " --> pdb=" O PHE D 409 " (cutoff:3.500A) 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 112 through 114 No H-bonds generated for 'chain 'E' and resid 112 through 114' Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 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: 4.455A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 294 removed outlier: 4.518A pdb=" N SER E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 330 Processing helix chain 'E' and resid 451 through 473 removed outlier: 4.116A pdb=" N ALA E 457 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 460 - end of helix removed outlier: 3.907A pdb=" N PHE E 465 " --> pdb=" O PHE E 461 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 173 through 177 removed outlier: 6.321A pdb=" N VAL A 44 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLU A 176 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL A 46 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 68 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 55 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG A 66 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.985A pdb=" N LEU A 125 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 105 through 107 removed outlier: 5.999A pdb=" N THR A 215 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.987A 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: 3.613A 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: 6.413A pdb=" N VAL B 44 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N GLU B 176 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B 46 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN B 45 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN B 76 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 68 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 55 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 66 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= G, first strand: chain 'B' and resid 105 through 107 Processing sheet with id= H, first strand: chain 'B' and resid 201 through 203 Processing sheet with id= I, first strand: chain 'C' and resid 173 through 176 removed outlier: 6.110A pdb=" N VAL C 44 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLU C 176 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL C 46 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASN C 45 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN C 76 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN C 68 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE C 55 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG C 66 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 125 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 92 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 105 through 107 Processing sheet with id= K, first strand: chain 'C' and resid 201 through 204 Processing sheet with id= L, first strand: chain 'C' and resid 110 through 115 removed outlier: 6.652A pdb=" N THR C 142 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 113 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 140 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 173 through 177 removed outlier: 6.300A pdb=" N VAL D 44 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU D 176 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL D 46 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN D 45 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASN D 76 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN D 68 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE D 55 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG D 66 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU D 125 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 50 through 52 removed outlier: 3.765A pdb=" N GLN D 184 " --> pdb=" O ILE D 50 " (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: 6.555A pdb=" N THR D 142 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA D 113 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.630A 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: 6.290A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR E 79 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU E 141 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 199 through 201 removed outlier: 6.991A pdb=" N ILE E 64 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 121 through 123 removed outlier: 3.572A pdb=" N ARG E 241 " --> pdb=" O ASP E 210 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1632 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: 3.90 Time building geometry restraints manager: 5.86 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: 3463 1.33 - 1.46: 3094 1.46 - 1.58: 7274 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 13966 Sorted by residual: bond pdb=" N VAL D 58 " pdb=" CA VAL D 58 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 9.86e+00 bond pdb=" N GLY B 203 " pdb=" CA GLY B 203 " ideal model delta sigma weight residual 1.443 1.480 -0.037 1.17e-02 7.31e+03 9.85e+00 bond pdb=" C ALA A 256 " pdb=" N PRO A 257 " ideal model delta sigma weight residual 1.337 1.368 -0.032 1.06e-02 8.90e+03 8.88e+00 bond pdb=" N LYS B 207 " pdb=" CA LYS B 207 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.25e-02 6.40e+03 8.78e+00 bond pdb=" N ILE D 264 " pdb=" CA ILE D 264 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.34e+00 ... (remaining 13961 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.22: 434 106.22 - 113.26: 7548 113.26 - 120.29: 5238 120.29 - 127.33: 5650 127.33 - 134.36: 179 Bond angle restraints: 19049 Sorted by residual: angle pdb=" C TYR C 235 " pdb=" N ILE C 236 " pdb=" CA ILE C 236 " ideal model delta sigma weight residual 120.24 123.39 -3.15 6.30e-01 2.52e+00 2.50e+01 angle pdb=" C TYR B 235 " pdb=" N ILE B 236 " pdb=" CA ILE B 236 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.15e+01 angle pdb=" N THR E 166 " pdb=" CA THR E 166 " pdb=" C THR E 166 " ideal model delta sigma weight residual 113.30 107.27 6.03 1.34e+00 5.57e-01 2.03e+01 angle pdb=" C VAL C 118 " pdb=" N THR C 119 " pdb=" CA THR C 119 " ideal model delta sigma weight residual 121.54 129.82 -8.28 1.91e+00 2.74e-01 1.88e+01 angle pdb=" N ALA A 256 " pdb=" CA ALA A 256 " pdb=" C ALA A 256 " ideal model delta sigma weight residual 109.81 118.92 -9.11 2.21e+00 2.05e-01 1.70e+01 ... (remaining 19044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.66: 7892 20.66 - 41.32: 605 41.32 - 61.98: 92 61.98 - 82.64: 17 82.64 - 103.30: 7 Dihedral angle restraints: 8613 sinusoidal: 3628 harmonic: 4985 Sorted by residual: dihedral pdb=" CA CYS E 175 " pdb=" C CYS E 175 " pdb=" N LYS E 176 " pdb=" CA LYS E 176 " ideal model delta harmonic sigma weight residual -180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 175 " pdb=" CB CYS E 175 " ideal model delta sinusoidal sigma weight residual -86.00 -39.07 -46.93 1 1.00e+01 1.00e-02 3.04e+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 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 8610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1973 0.086 - 0.172: 198 0.172 - 0.259: 16 0.259 - 0.345: 13 0.345 - 0.431: 7 Chirality restraints: 2207 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 -1.97 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" NAY SY9 A 503 " pdb=" CAS SY9 A 503 " pdb=" CAV SY9 A 503 " pdb=" CAX SY9 A 503 " both_signs ideal model delta sigma weight residual False -2.12 -2.54 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" NAY SY9 D 504 " pdb=" CAS SY9 D 504 " pdb=" CAV SY9 D 504 " pdb=" CAX SY9 D 504 " both_signs ideal model delta sigma weight residual False -2.12 -2.53 0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 2204 not shown) Planarity restraints: 2354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 45 " -0.006 2.00e-02 2.50e+03 2.50e-02 7.81e+00 pdb=" CG ASN C 45 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 45 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN C 45 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG C 501 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 193 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C GLN D 193 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN D 193 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE D 194 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 134 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C VAL E 134 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL E 134 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 135 " 0.015 2.00e-02 2.50e+03 ... (remaining 2351 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2373 2.77 - 3.30: 12424 3.30 - 3.83: 22146 3.83 - 4.37: 25198 4.37 - 4.90: 45082 Nonbonded interactions: 107223 Sorted by model distance: nonbonded pdb=" OG SER B 285 " pdb=" O GLN C 226 " model vdw 2.232 2.440 nonbonded pdb=" O ALA A 289 " pdb=" OH TYR A 410 " model vdw 2.233 2.440 nonbonded pdb=" O PHE B 409 " pdb=" OG1 THR B 413 " model vdw 2.242 2.440 nonbonded pdb=" O ASP B 121 " pdb=" OD1 ASP B 121 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR E 185 " pdb=" OD1 ASP E 187 " model vdw 2.252 2.440 ... (remaining 107218 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: 0.760 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: 4.310 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 36.590 Find NCS groups from input model: 0.820 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.005 0.052 13966 Z= 0.347 Angle : 0.904 11.118 19049 Z= 0.472 Chirality : 0.061 0.431 2207 Planarity : 0.006 0.062 2345 Dihedral : 14.722 103.296 5361 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.28 % Allowed : 10.68 % Favored : 89.04 % 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: -4.07 (0.17), residues: 1666 helix: -1.41 (0.18), residues: 561 sheet: -3.12 (0.21), residues: 434 loop : -3.41 (0.20), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 293 HIS 0.003 0.001 HIS E 132 PHE 0.025 0.002 PHE B 70 TYR 0.019 0.002 TYR E 303 ARG 0.005 0.000 ARG E 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 302 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 306 average time/residue: 0.2689 time to fit residues: 116.7842 Evaluate side-chains 238 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 1.591 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1179 time to fit residues: 2.8288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 30.0000 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 0.1980 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 233 GLN A 252 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN B 74 GLN B 233 GLN B 252 ASN C 74 GLN C 222 HIS C 233 GLN C 273 GLN D 233 GLN D 312 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13966 Z= 0.259 Angle : 0.651 9.871 19049 Z= 0.320 Chirality : 0.045 0.373 2207 Planarity : 0.004 0.051 2345 Dihedral : 7.330 61.742 2324 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.81 % Allowed : 18.10 % Favored : 78.09 % 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: -2.89 (0.19), residues: 1666 helix: 0.04 (0.21), residues: 566 sheet: -2.75 (0.22), residues: 427 loop : -3.02 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 246 HIS 0.002 0.001 HIS C 208 PHE 0.018 0.001 PHE E 319 TYR 0.018 0.002 TYR E 303 ARG 0.008 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 244 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 41 residues processed: 275 average time/residue: 0.2471 time to fit residues: 99.4584 Evaluate side-chains 262 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 221 time to evaluate : 1.440 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 41 outliers final: 1 residues processed: 41 average time/residue: 0.1256 time to fit residues: 11.5141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 162 optimal weight: 0.4980 chunk 133 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 208 HIS A 233 GLN A 252 ASN A 273 GLN A 407 ASN C 233 GLN D 273 GLN D 312 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13966 Z= 0.142 Angle : 0.593 9.502 19049 Z= 0.290 Chirality : 0.043 0.393 2207 Planarity : 0.004 0.059 2345 Dihedral : 5.975 59.994 2324 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.70 % Allowed : 21.29 % Favored : 76.01 % 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: -2.14 (0.20), residues: 1666 helix: 0.86 (0.22), residues: 554 sheet: -2.20 (0.24), residues: 414 loop : -2.84 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 246 HIS 0.003 0.000 HIS D 222 PHE 0.032 0.001 PHE D 249 TYR 0.024 0.001 TYR A 85 ARG 0.005 0.000 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 256 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 16 residues processed: 280 average time/residue: 0.2257 time to fit residues: 96.6007 Evaluate side-chains 242 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 226 time to evaluate : 1.480 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.1205 time to fit residues: 5.8061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 252 ASN A 273 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN D 273 GLN E 67 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13966 Z= 0.272 Angle : 0.628 9.671 19049 Z= 0.308 Chirality : 0.044 0.308 2207 Planarity : 0.004 0.065 2345 Dihedral : 5.935 57.725 2324 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.12 % Allowed : 23.79 % Favored : 73.09 % 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: -1.95 (0.21), residues: 1666 helix: 0.96 (0.22), residues: 566 sheet: -2.24 (0.23), residues: 429 loop : -2.61 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 246 HIS 0.002 0.001 HIS E 132 PHE 0.019 0.001 PHE A 302 TYR 0.017 0.002 TYR E 303 ARG 0.004 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 230 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 30 residues processed: 257 average time/residue: 0.2338 time to fit residues: 90.7091 Evaluate side-chains 251 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 1.684 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 30 outliers final: 1 residues processed: 30 average time/residue: 0.1345 time to fit residues: 10.0748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.1980 chunk 90 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 208 HIS B 53 ASN C 233 GLN D 312 ASN E 132 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13966 Z= 0.303 Angle : 0.638 9.971 19049 Z= 0.315 Chirality : 0.044 0.301 2207 Planarity : 0.004 0.051 2345 Dihedral : 5.955 57.434 2324 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.91 % Allowed : 24.90 % Favored : 72.19 % 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: -1.84 (0.21), residues: 1666 helix: 1.05 (0.22), residues: 566 sheet: -2.14 (0.24), residues: 422 loop : -2.56 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 246 HIS 0.002 0.001 HIS E 132 PHE 0.015 0.001 PHE E 69 TYR 0.022 0.002 TYR A 85 ARG 0.005 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 229 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 25 residues processed: 258 average time/residue: 0.2243 time to fit residues: 88.3020 Evaluate side-chains 245 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 1.543 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.1209 time to fit residues: 7.6093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 159 optimal weight: 0.8980 chunk 132 optimal weight: 0.2980 chunk 73 optimal weight: 0.0470 chunk 13 optimal weight: 0.0270 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 157 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN D 68 ASN D 312 ASN E 132 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13966 Z= 0.142 Angle : 0.596 9.908 19049 Z= 0.289 Chirality : 0.043 0.285 2207 Planarity : 0.004 0.047 2345 Dihedral : 5.652 58.909 2324 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.08 % Allowed : 25.31 % Favored : 72.61 % 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: -1.46 (0.21), residues: 1666 helix: 1.31 (0.23), residues: 561 sheet: -1.80 (0.24), residues: 418 loop : -2.38 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 246 HIS 0.001 0.000 HIS C 208 PHE 0.024 0.001 PHE B 302 TYR 0.017 0.001 TYR E 303 ARG 0.004 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 247 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 268 average time/residue: 0.2287 time to fit residues: 92.6733 Evaluate side-chains 241 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 225 time to evaluate : 1.527 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.1319 time to fit residues: 5.9799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 134 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 30.0000 chunk 73 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 overall best weight: 1.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS D 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13966 Z= 0.190 Angle : 0.603 9.693 19049 Z= 0.293 Chirality : 0.044 0.432 2207 Planarity : 0.004 0.046 2345 Dihedral : 5.618 58.524 2324 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.87 % Allowed : 26.07 % Favored : 72.05 % 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: -1.36 (0.21), residues: 1666 helix: 1.36 (0.23), residues: 561 sheet: -1.76 (0.24), residues: 426 loop : -2.27 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 246 HIS 0.002 0.000 HIS D 222 PHE 0.023 0.001 PHE E 319 TYR 0.021 0.001 TYR A 85 ARG 0.004 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 232 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 246 average time/residue: 0.2322 time to fit residues: 85.6660 Evaluate side-chains 241 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 224 time to evaluate : 1.594 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.1292 time to fit residues: 6.1871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.2980 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 125 optimal weight: 0.0870 chunk 144 optimal weight: 0.9980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13966 Z= 0.143 Angle : 0.592 9.564 19049 Z= 0.287 Chirality : 0.043 0.357 2207 Planarity : 0.004 0.047 2345 Dihedral : 5.475 59.006 2324 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.76 % Allowed : 27.18 % Favored : 72.05 % 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: 1666 helix: 1.55 (0.23), residues: 553 sheet: -1.60 (0.25), residues: 426 loop : -2.20 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 246 HIS 0.001 0.000 HIS D 222 PHE 0.015 0.001 PHE E 319 TYR 0.017 0.001 TYR E 303 ARG 0.004 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 236 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 241 average time/residue: 0.2437 time to fit residues: 87.4956 Evaluate side-chains 231 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 224 time to evaluate : 1.597 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1345 time to fit residues: 3.8825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 0.0040 chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 overall best weight: 0.9872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN E 67 ASN E 132 HIS E 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13966 Z= 0.158 Angle : 0.592 9.563 19049 Z= 0.287 Chirality : 0.043 0.310 2207 Planarity : 0.004 0.046 2345 Dihedral : 5.447 58.990 2324 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.32 % Allowed : 27.12 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1666 helix: 1.57 (0.23), residues: 557 sheet: -1.50 (0.25), residues: 426 loop : -2.12 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 246 HIS 0.002 0.000 HIS D 222 PHE 0.022 0.001 PHE B 20 TYR 0.014 0.001 TYR C 286 ARG 0.006 0.000 ARG E 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 231 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 238 average time/residue: 0.2395 time to fit residues: 85.0340 Evaluate side-chains 238 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 224 time to evaluate : 1.378 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.1262 time to fit residues: 5.4862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 80 optimal weight: 0.0570 chunk 103 optimal weight: 7.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 233 GLN D 312 ASN E 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13966 Z= 0.182 Angle : 0.606 9.598 19049 Z= 0.294 Chirality : 0.043 0.296 2207 Planarity : 0.004 0.046 2345 Dihedral : 5.474 58.800 2324 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.62 % Allowed : 27.81 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1666 helix: 1.62 (0.23), residues: 557 sheet: -1.45 (0.25), residues: 426 loop : -2.07 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 246 HIS 0.002 0.000 HIS E 132 PHE 0.014 0.001 PHE D 403 TYR 0.016 0.001 TYR E 303 ARG 0.004 0.000 ARG C 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 227 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 234 average time/residue: 0.2518 time to fit residues: 86.8343 Evaluate side-chains 225 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 1.690 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1549 time to fit residues: 3.3126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 134 optimal weight: 0.0770 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN E 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112363 restraints weight = 19467.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.115330 restraints weight = 11914.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117302 restraints weight = 8606.756| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13966 Z= 0.156 Angle : 0.591 9.550 19049 Z= 0.287 Chirality : 0.043 0.273 2207 Planarity : 0.004 0.046 2345 Dihedral : 5.437 58.971 2324 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.90 % Allowed : 27.81 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1666 helix: 1.67 (0.23), residues: 557 sheet: -1.34 (0.25), residues: 425 loop : -2.04 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 246 HIS 0.002 0.000 HIS D 222 PHE 0.026 0.001 PHE B 20 TYR 0.014 0.001 TYR C 286 ARG 0.003 0.000 ARG C 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2766.46 seconds wall clock time: 51 minutes 18.35 seconds (3078.35 seconds total)