Starting phenix.real_space_refine (version: dev) on Tue Apr 5 19:06:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/04_2022/6i53_4411_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/04_2022/6i53_4411.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/04_2022/6i53_4411_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/04_2022/6i53_4411_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/04_2022/6i53_4411_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/04_2022/6i53_4411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/04_2022/6i53_4411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/04_2022/6i53_4411_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/04_2022/6i53_4411_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E ARG 180": "NH1" <-> "NH2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 406": "NH1" <-> "NH2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 15362 Number of models: 1 Model: "" Number of chains: 11 Chain: "E" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2754 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'CIS': 1, 'TRANS': 319, 'PCIS': 1} Chain breaks: 1 Chain: "A" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2823 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 12, 'CIS': 1, 'TRANS': 334, 'PCIS': 1} Chain breaks: 1 Chain: "B" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2770 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'CIS': 1, 'TRANS': 321, 'PCIS': 1} Chain breaks: 1 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2701 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 11, 'CIS': 1, 'TRANS': 314, 'PCIS': 1} Chain breaks: 1 Chain: "D" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2805 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 12, 'CIS': 1, 'TRANS': 332, 'PCIS': 1} Chain breaks: 1 Chain: "G" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 949 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 124 Unusual residues: {'POV': 1, 'BMA': 1, 'NAG': 4, 'MAN': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 165 Unusual residues: {'MAN': 4, 'POV': 1, 'BMA': 1, 'NAG': 2, 'PIO': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 100 Unusual residues: {'BMA': 1, 'NAG': 4, 'MAN': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Unusual residues: {'MAN': 2, 'POV': 1, 'BMA': 1, 'NAG': 2, 'PIO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 8.83, per 1000 atoms: 0.57 Number of scatterers: 15362 At special positions: 0 Unit cell: (97.37, 123.05, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 9 15.00 O 2854 8.00 N 2474 7.00 C 9943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " 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 ALPHA1-3 " BMA A 604 " - " MAN A 608 " " MAN A 605 " - " MAN A 607 " " BMA B 503 " - " MAN B 506 " " MAN B 504 " - " MAN B 505 " " BMA D 504 " - " MAN D 506 " " BMA E 503 " - " MAN E 505 " ALPHA1-6 " BMA A 604 " - " MAN A 605 " " MAN A 605 " - " MAN A 606 " " BMA B 503 " - " MAN B 504 " " BMA D 504 " - " MAN D 505 " " BMA E 503 " - " MAN E 504 " BETA1-4 " NAG A 602 " - " NAG A 603 " " NAG A 603 " - " BMA A 604 " " NAG B 501 " - " NAG B 502 " " NAG B 502 " - " BMA B 503 " " NAG B 507 " - " NAG B 508 " " NAG C3000 " - " NAG C3001 " " NAG D 502 " - " NAG D 503 " " NAG D 503 " - " BMA D 504 " " NAG E 501 " - " NAG E 502 " " NAG E 502 " - " BMA E 503 " " NAG E 506 " - " NAG E 507 " NAG-ASN " NAG A 602 " - " ASN A 111 " " NAG B 501 " - " ASN B 149 " " NAG B 507 " - " ASN B 80 " " NAG C3000 " - " ASN C 208 " " NAG D 502 " - " ASN D 111 " " NAG E 501 " - " ASN E 149 " " NAG E 506 " - " ASN E 80 " Time building additional restraints: 6.48 Conformation dependent library (CDL) restraints added in 2.3 seconds 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3446 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 24 sheets defined 31.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'E' and resid 11 through 19 removed outlier: 3.547A pdb=" N ASP E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.530A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 219 through 224 removed outlier: 3.998A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 240 removed outlier: 3.717A pdb=" N LEU E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 266 removed outlier: 3.681A pdb=" N ALA E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 282 through 307 removed outlier: 3.648A pdb=" N PHE E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE E 307 " --> pdb=" O ASN E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 445 removed outlier: 3.680A pdb=" N ASP E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 431 " --> pdb=" O SER E 427 " (cutoff:3.500A) Proline residue: E 432 - end of helix removed outlier: 3.636A pdb=" N SER E 436 " --> pdb=" O PRO E 432 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.730A pdb=" N ILE A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 252 through 271 removed outlier: 4.754A pdb=" N VAL A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 removed outlier: 4.031A pdb=" N VAL A 292 " --> pdb=" O TRP A 288 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 297 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.732A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Proline residue: A 401 - end of helix removed outlier: 4.175A pdb=" N TRP A 412 " --> pdb=" O ASN A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 removed outlier: 3.625A pdb=" N LYS B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.523A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.223A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 removed outlier: 3.560A pdb=" N THR B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.832A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 305 removed outlier: 3.612A pdb=" N MET B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 445 removed outlier: 3.730A pdb=" N ASP B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.889A pdb=" N SER B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 235 through 239 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.705A pdb=" N SER C 254 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 255 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 284 removed outlier: 3.738A pdb=" N GLY C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 322 removed outlier: 3.586A pdb=" N ILE C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 307 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 432 removed outlier: 4.425A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.514A pdb=" N PHE C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 removed outlier: 3.633A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.772A pdb=" N VAL D 227 " --> pdb=" O GLY D 224 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 228 " --> pdb=" O TYR D 225 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN D 229 " --> pdb=" O PHE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 removed outlier: 3.603A pdb=" N LEU D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 252 through 272 removed outlier: 4.641A pdb=" N VAL D 257 " --> pdb=" O PRO D 253 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL D 263 " --> pdb=" O GLY D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 287 through 310 removed outlier: 3.628A pdb=" N VAL D 292 " --> pdb=" O TRP D 288 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 414 removed outlier: 3.659A pdb=" N LEU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 3.540A pdb=" N GLY D 405 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 107 through 109 No H-bonds generated for 'chain 'G' and resid 107 through 109' Processing sheet with id= A, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.305A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 66 through 68 removed outlier: 4.477A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.748A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 186 through 188 Processing sheet with id= E, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.953A pdb=" N THR A 39 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU A 170 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL A 41 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 119 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= G, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.226A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 210 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.489A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 66 through 68 Processing sheet with id= J, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.521A pdb=" N CYS B 150 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 191 through 200 removed outlier: 3.650A pdb=" N GLY B 203 " --> pdb=" O PHE B 200 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.810A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 179 through 183 removed outlier: 5.870A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= O, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.702A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 218 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.762A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 167 through 171 removed outlier: 5.970A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP D 70 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 83 through 85 Processing sheet with id= S, first strand: chain 'D' and resid 150 through 158 Processing sheet with id= T, first strand: chain 'D' and resid 196 through 199 Processing sheet with id= U, first strand: chain 'D' and resid 202 through 204 Processing sheet with id= V, first strand: chain 'G' and resid 3 through 6 Processing sheet with id= W, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.495A pdb=" N THR G 120 " --> pdb=" O VAL G 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'G' and resid 117 through 119 removed outlier: 3.565A pdb=" N MET G 34 " --> pdb=" O MET G 51 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2299 1.30 - 1.43: 4524 1.43 - 1.56: 8729 1.56 - 1.68: 45 1.68 - 1.81: 147 Bond restraints: 15744 Sorted by residual: bond pdb=" C21 POV A 609 " pdb=" O21 POV A 609 " ideal model delta sigma weight residual 1.330 1.474 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C21 POV E 508 " pdb=" O21 POV E 508 " ideal model delta sigma weight residual 1.330 1.473 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C21 POV D 507 " pdb=" O21 POV D 507 " ideal model delta sigma weight residual 1.330 1.472 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C36 POV A 609 " pdb=" C37 POV A 609 " ideal model delta sigma weight residual 1.523 1.611 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C36 POV E 508 " pdb=" C37 POV E 508 " ideal model delta sigma weight residual 1.523 1.611 -0.088 2.00e-02 2.50e+03 1.94e+01 ... (remaining 15739 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.39: 295 105.39 - 112.55: 8180 112.55 - 119.71: 5143 119.71 - 126.86: 7554 126.86 - 134.02: 213 Bond angle restraints: 21385 Sorted by residual: angle pdb=" C GLY G 103 " pdb=" N LEU G 104 " pdb=" CA LEU G 104 " ideal model delta sigma weight residual 121.54 131.68 -10.14 1.91e+00 2.74e-01 2.82e+01 angle pdb=" C4 PIO A 601 " pdb=" O4 PIO A 601 " pdb=" P4 PIO A 601 " ideal model delta sigma weight residual 118.46 132.99 -14.53 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C4 PIO D 501 " pdb=" O4 PIO D 501 " pdb=" P4 PIO D 501 " ideal model delta sigma weight residual 118.46 132.03 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C ASP C 192 " pdb=" N THR C 193 " pdb=" CA THR C 193 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" N PRO D 175 " pdb=" CA PRO D 175 " pdb=" C PRO D 175 " ideal model delta sigma weight residual 112.47 120.66 -8.19 2.06e+00 2.36e-01 1.58e+01 ... (remaining 21380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 8955 17.24 - 34.48: 206 34.48 - 51.71: 58 51.71 - 68.95: 8 68.95 - 86.19: 7 Dihedral angle restraints: 9234 sinusoidal: 3874 harmonic: 5360 Sorted by residual: dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 150 " pdb=" CB CYS E 150 " ideal model delta sinusoidal sigma weight residual 93.00 161.27 -68.27 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA GLU D 174 " pdb=" C GLU D 174 " pdb=" N PRO D 175 " pdb=" CA PRO D 175 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA PRO D 154 " pdb=" C PRO D 154 " pdb=" N LEU D 155 " pdb=" CA LEU D 155 " ideal model delta harmonic sigma weight residual 180.00 156.96 23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 9231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2236 0.081 - 0.162: 238 0.162 - 0.243: 7 0.243 - 0.324: 2 0.324 - 0.405: 1 Chirality restraints: 2484 Sorted by residual: chirality pdb=" C1 NAG D 502 " pdb=" ND2 ASN D 111 " pdb=" C2 NAG D 502 " pdb=" O5 NAG D 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" C1 NAG C3000 " pdb=" ND2 ASN C 208 " pdb=" C2 NAG C3000 " pdb=" O5 NAG C3000 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 149 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2481 not shown) Planarity restraints: 2603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 502 " -0.051 2.00e-02 2.50e+03 4.21e-02 2.22e+01 pdb=" C7 NAG D 502 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG D 502 " -0.040 2.00e-02 2.50e+03 pdb=" N2 NAG D 502 " 0.065 2.00e-02 2.50e+03 pdb=" O7 NAG D 502 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " -0.030 2.00e-02 2.50e+03 2.49e-02 7.76e+00 pdb=" C7 NAG A 602 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " 0.039 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 431 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO B 432 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " -0.036 5.00e-02 4.00e+02 ... (remaining 2600 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3762 2.79 - 3.32: 12762 3.32 - 3.85: 25095 3.85 - 4.37: 30613 4.37 - 4.90: 52209 Nonbonded interactions: 124441 Sorted by model distance: nonbonded pdb=" O THR D 172 " pdb=" OG SER D 178 " model vdw 2.264 2.440 nonbonded pdb=" O ALA E 280 " pdb=" OH TYR E 442 " model vdw 2.326 2.440 nonbonded pdb=" NE2 HIS A 110 " pdb=" OG1 THR A 134 " model vdw 2.327 2.520 nonbonded pdb=" OH TYR A 60 " pdb=" O PRO A 154 " model vdw 2.332 2.440 nonbonded pdb=" NE2 HIS D 110 " pdb=" OG1 THR D 134 " model vdw 2.335 2.520 ... (remaining 124436 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 10 through 322 or resid 384 through 417 or resid 607 throu \ gh 609)) selection = (chain 'D' and (resid 10 through 417 or resid 505 through 507)) } ncs_group { reference = (chain 'B' and (resid 10 through 447 or resid 501 through 505 or resid 507)) selection = (chain 'E' and (resid 10 through 447 or resid 501 through 505 or resid 507)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 82 5.16 5 C 9943 2.51 5 N 2474 2.21 5 O 2854 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic 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: 1.280 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: 4.760 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.110 Process input model: 42.100 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 0.144 15744 Z= 0.412 Angle : 0.883 14.535 21385 Z= 0.439 Chirality : 0.050 0.405 2484 Planarity : 0.007 0.063 2596 Dihedral : 9.183 86.191 5770 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -4.72 (0.15), residues: 1799 helix: -4.37 (0.08), residues: 537 sheet: -2.48 (0.20), residues: 494 loop : -2.39 (0.19), residues: 768 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 1.753 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.3258 time to fit residues: 210.9245 Evaluate side-chains 273 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.808 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 303 ASN E 421 ASN A 308 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 113 ASN B 217 ASN B 303 ASN B 421 ASN C 80 GLN C 128 ASN C 323 ASN D 56 HIS D 151 HIS G 111 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 15744 Z= 0.200 Angle : 0.561 7.854 21385 Z= 0.296 Chirality : 0.043 0.304 2484 Planarity : 0.005 0.071 2596 Dihedral : 8.184 89.052 2368 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -2.98 (0.18), residues: 1799 helix: -1.99 (0.18), residues: 521 sheet: -1.91 (0.22), residues: 482 loop : -1.83 (0.21), residues: 796 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 294 time to evaluate : 1.978 Fit side-chains outliers start: 29 outliers final: 14 residues processed: 310 average time/residue: 0.2863 time to fit residues: 129.6540 Evaluate side-chains 273 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 259 time to evaluate : 1.782 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1424 time to fit residues: 6.1708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 174 optimal weight: 0.0370 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 ASN E 303 ASN A 190 GLN A 308 ASN A 387 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN B 303 ASN C 152 GLN C 182 GLN D 56 HIS G 111 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15744 Z= 0.239 Angle : 0.536 6.644 21385 Z= 0.280 Chirality : 0.042 0.284 2484 Planarity : 0.004 0.040 2596 Dihedral : 7.833 89.787 2368 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -2.07 (0.19), residues: 1799 helix: -0.81 (0.21), residues: 524 sheet: -1.52 (0.22), residues: 481 loop : -1.51 (0.22), residues: 794 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 265 time to evaluate : 1.754 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 275 average time/residue: 0.2880 time to fit residues: 115.7788 Evaluate side-chains 253 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 241 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1410 time to fit residues: 5.5270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 0.0770 chunk 143 optimal weight: 0.7980 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 ASN A 68 GLN C 152 GLN C 182 GLN C 323 ASN D 56 HIS G 111 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 15744 Z= 0.248 Angle : 0.522 6.621 21385 Z= 0.272 Chirality : 0.042 0.285 2484 Planarity : 0.004 0.043 2596 Dihedral : 7.591 89.315 2368 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -1.56 (0.19), residues: 1799 helix: -0.16 (0.23), residues: 517 sheet: -1.36 (0.22), residues: 484 loop : -1.29 (0.22), residues: 798 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 251 time to evaluate : 1.619 Fit side-chains outliers start: 28 outliers final: 22 residues processed: 265 average time/residue: 0.3008 time to fit residues: 114.9516 Evaluate side-chains 254 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 232 time to evaluate : 1.817 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1361 time to fit residues: 8.0425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 113 ASN C 152 GLN C 323 ASN G 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 15744 Z= 0.304 Angle : 0.548 6.749 21385 Z= 0.284 Chirality : 0.043 0.288 2484 Planarity : 0.004 0.065 2596 Dihedral : 7.595 89.929 2368 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -1.31 (0.19), residues: 1799 helix: 0.14 (0.23), residues: 519 sheet: -1.20 (0.22), residues: 475 loop : -1.23 (0.22), residues: 805 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 242 time to evaluate : 1.664 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 247 average time/residue: 0.3044 time to fit residues: 108.1349 Evaluate side-chains 237 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 231 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2006 time to fit residues: 4.6141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 172 optimal weight: 0.2980 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 ASN C 152 GLN C 323 ASN D 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 15744 Z= 0.298 Angle : 0.539 6.676 21385 Z= 0.280 Chirality : 0.043 0.286 2484 Planarity : 0.004 0.044 2596 Dihedral : 7.467 89.498 2368 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -1.14 (0.20), residues: 1799 helix: 0.35 (0.23), residues: 524 sheet: -1.11 (0.23), residues: 475 loop : -1.17 (0.22), residues: 800 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 238 time to evaluate : 1.845 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 245 average time/residue: 0.3094 time to fit residues: 108.8403 Evaluate side-chains 237 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 229 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1375 time to fit residues: 4.5470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 0.0050 chunk 144 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 171 optimal weight: 0.2980 chunk 107 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN C 152 GLN C 323 ASN D 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 15744 Z= 0.165 Angle : 0.491 7.360 21385 Z= 0.254 Chirality : 0.041 0.272 2484 Planarity : 0.003 0.036 2596 Dihedral : 7.116 87.677 2368 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.80 (0.20), residues: 1799 helix: 0.70 (0.23), residues: 524 sheet: -0.90 (0.23), residues: 467 loop : -1.04 (0.22), residues: 808 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 250 time to evaluate : 1.858 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 256 average time/residue: 0.3125 time to fit residues: 115.2190 Evaluate side-chains 239 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 233 time to evaluate : 1.963 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1828 time to fit residues: 4.3426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 0.0980 chunk 15 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 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 190 GLN B 113 ASN C 152 GLN C 323 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 15744 Z= 0.263 Angle : 0.522 7.072 21385 Z= 0.270 Chirality : 0.043 0.281 2484 Planarity : 0.004 0.060 2596 Dihedral : 7.163 89.233 2368 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.73 (0.20), residues: 1799 helix: 0.69 (0.23), residues: 530 sheet: -0.85 (0.23), residues: 463 loop : -0.97 (0.22), residues: 806 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 238 time to evaluate : 1.739 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 242 average time/residue: 0.3009 time to fit residues: 105.2174 Evaluate side-chains 239 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 233 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1304 time to fit residues: 3.8615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 125 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 113 ASN C 152 GLN C 323 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 15744 Z= 0.209 Angle : 0.507 7.854 21385 Z= 0.261 Chirality : 0.042 0.272 2484 Planarity : 0.004 0.046 2596 Dihedral : 7.069 88.449 2368 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.59 (0.20), residues: 1799 helix: 0.88 (0.23), residues: 525 sheet: -0.79 (0.23), residues: 464 loop : -0.90 (0.22), residues: 810 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 237 time to evaluate : 1.872 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 239 average time/residue: 0.3080 time to fit residues: 106.2894 Evaluate side-chains 231 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1417 time to fit residues: 2.9803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 117 optimal weight: 0.3980 chunk 177 optimal weight: 0.0980 chunk 163 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN C 152 GLN C 323 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.149 15744 Z= 0.204 Angle : 0.505 11.219 21385 Z= 0.264 Chirality : 0.041 0.267 2484 Planarity : 0.004 0.116 2596 Dihedral : 6.925 87.709 2368 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.45 (0.20), residues: 1799 helix: 1.00 (0.24), residues: 527 sheet: -0.71 (0.23), residues: 464 loop : -0.83 (0.22), residues: 808 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 238 time to evaluate : 1.744 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 240 average time/residue: 0.3074 time to fit residues: 106.9213 Evaluate side-chains 238 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 1.927 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1745 time to fit residues: 3.3439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 145 optimal weight: 0.3980 chunk 17 optimal weight: 0.4980 chunk 26 optimal weight: 0.1980 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN C 152 GLN C 323 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.098171 restraints weight = 20201.660| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.78 r_work: 0.3040 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 1.57 restraints_weight: 0.2500 r_work: 0.3013 rms_B_bonded: 1.62 restraints_weight: 0.1250 r_work: 0.2999 rms_B_bonded: 1.73 restraints_weight: 0.0625 r_work: 0.2983 rms_B_bonded: 1.87 restraints_weight: 0.0312 r_work: 0.2965 rms_B_bonded: 2.07 restraints_weight: 0.0156 r_work: 0.2946 rms_B_bonded: 2.31 restraints_weight: 0.0078 r_work: 0.2924 rms_B_bonded: 2.60 restraints_weight: 0.0039 r_work: 0.2900 rms_B_bonded: 2.96 restraints_weight: 0.0020 r_work: 0.2873 rms_B_bonded: 3.38 restraints_weight: 0.0010 r_work: 0.2842 rms_B_bonded: 3.88 restraints_weight: 0.0005 r_work: 0.2807 rms_B_bonded: 4.47 restraints_weight: 0.0002 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.107 15744 Z= 0.171 Angle : 0.497 8.876 21385 Z= 0.257 Chirality : 0.041 0.265 2484 Planarity : 0.004 0.095 2596 Dihedral : 6.787 87.200 2368 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.30 (0.20), residues: 1799 helix: 1.10 (0.24), residues: 529 sheet: -0.65 (0.23), residues: 464 loop : -0.71 (0.22), residues: 806 =============================================================================== Job complete usr+sys time: 3185.32 seconds wall clock time: 58 minutes 51.12 seconds (3531.12 seconds total)