Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 03:13:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/04_2023/7cqi_30441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/04_2023/7cqi_30441.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/04_2023/7cqi_30441_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/7cqi_30441/04_2023/7cqi_30441_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/04_2023/7cqi_30441_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/04_2023/7cqi_30441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/04_2023/7cqi_30441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/04_2023/7cqi_30441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/04_2023/7cqi_30441_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 Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 51 5.16 5 C 5719 2.51 5 N 1486 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S ASP 76": "OD1" <-> "OD2" Residue "S PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 116": "NH1" <-> "NH2" Residue "S ARG 151": "NH1" <-> "NH2" Residue "S TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 189": "NH1" <-> "NH2" Residue "S ARG 203": "NH1" <-> "NH2" Residue "S ARG 236": "NH1" <-> "NH2" Residue "S ARG 239": "NH1" <-> "NH2" Residue "S TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 270": "NH1" <-> "NH2" Residue "S ARG 287": "NH1" <-> "NH2" Residue "S ARG 329": "NH1" <-> "NH2" Residue "S PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 405": "NH1" <-> "NH2" Residue "S ARG 459": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 106": "OE1" <-> "OE2" Residue "T ARG 129": "NH1" <-> "NH2" Residue "T ARG 151": "NH1" <-> "NH2" Residue "T TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 207": "NH1" <-> "NH2" Residue "T ARG 278": "NH1" <-> "NH2" Residue "T TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 326": "NH1" <-> "NH2" Residue "T TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 447": "NH1" <-> "NH2" Residue "T ARG 450": "NH1" <-> "NH2" Residue "T ARG 489": "NH1" <-> "NH2" Residue "T ARG 507": "NH1" <-> "NH2" Residue "T ARG 509": "NH1" <-> "NH2" Residue "T TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "C ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8881 Number of models: 1 Model: "" Number of chains: 6 Chain: "S" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3268 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 399} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3926 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 479} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1028 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 182 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "T" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'GE0': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 5.24, per 1000 atoms: 0.59 Number of scatterers: 8881 At special positions: 0 Unit cell: (91.8, 85.32, 118.8, 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 51 16.00 P 4 15.00 O 1621 8.00 N 1486 7.00 C 5719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.5 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 6 sheets defined 36.6% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'S' and resid 55 through 63 removed outlier: 3.518A pdb=" N GLU S 59 " --> pdb=" O LYS S 55 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU S 62 " --> pdb=" O GLU S 58 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU S 63 " --> pdb=" O GLU S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 80 No H-bonds generated for 'chain 'S' and resid 78 through 80' Processing helix chain 'S' and resid 115 through 120 Processing helix chain 'S' and resid 145 through 155 removed outlier: 3.725A pdb=" N ARG S 151 " --> pdb=" O ASP S 147 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA S 153 " --> pdb=" O GLU S 149 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS S 154 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 172 No H-bonds generated for 'chain 'S' and resid 169 through 172' Processing helix chain 'S' and resid 193 through 201 removed outlier: 3.554A pdb=" N ALA S 201 " --> pdb=" O LYS S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 214 through 229 removed outlier: 3.875A pdb=" N GLU S 223 " --> pdb=" O ARG S 219 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN S 224 " --> pdb=" O LEU S 220 " (cutoff:3.500A) Processing helix chain 'S' and resid 258 through 261 No H-bonds generated for 'chain 'S' and resid 258 through 261' Processing helix chain 'S' and resid 290 through 293 No H-bonds generated for 'chain 'S' and resid 290 through 293' Processing helix chain 'S' and resid 297 through 299 No H-bonds generated for 'chain 'S' and resid 297 through 299' Processing helix chain 'S' and resid 325 through 331 removed outlier: 4.016A pdb=" N GLN S 328 " --> pdb=" O ILE S 325 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG S 329 " --> pdb=" O ASP S 326 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU S 330 " --> pdb=" O HIS S 327 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER S 331 " --> pdb=" O GLN S 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 325 through 331' Processing helix chain 'S' and resid 333 through 336 No H-bonds generated for 'chain 'S' and resid 333 through 336' Processing helix chain 'S' and resid 347 through 358 removed outlier: 3.546A pdb=" N GLU S 351 " --> pdb=" O ALA S 347 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU S 357 " --> pdb=" O LEU S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 364 through 367 No H-bonds generated for 'chain 'S' and resid 364 through 367' Processing helix chain 'S' and resid 369 through 375 removed outlier: 3.991A pdb=" N ILE S 373 " --> pdb=" O LYS S 369 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS S 374 " --> pdb=" O CYS S 370 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS S 375 " --> pdb=" O GLY S 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 369 through 375' Processing helix chain 'S' and resid 406 through 421 removed outlier: 3.559A pdb=" N LEU S 412 " --> pdb=" O ASP S 408 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU S 414 " --> pdb=" O ARG S 410 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE S 415 " --> pdb=" O LEU S 411 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET S 420 " --> pdb=" O VAL S 416 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN S 421 " --> pdb=" O ASP S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 454 through 468 Processing helix chain 'T' and resid 70 through 90 removed outlier: 4.198A pdb=" N TYR T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL T 80 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 133 No H-bonds generated for 'chain 'T' and resid 131 through 133' Processing helix chain 'T' and resid 178 through 180 No H-bonds generated for 'chain 'T' and resid 178 through 180' Processing helix chain 'T' and resid 195 through 198 No H-bonds generated for 'chain 'T' and resid 195 through 198' Processing helix chain 'T' and resid 215 through 227 removed outlier: 3.574A pdb=" N GLU T 220 " --> pdb=" O HIS T 216 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU T 222 " --> pdb=" O GLU T 218 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA T 224 " --> pdb=" O GLU T 220 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG T 225 " --> pdb=" O GLU T 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 242 through 249 Proline residue: T 247 - end of helix Processing helix chain 'T' and resid 264 through 271 Processing helix chain 'T' and resid 285 through 297 removed outlier: 4.056A pdb=" N ALA T 295 " --> pdb=" O LEU T 291 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE T 296 " --> pdb=" O LEU T 292 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL T 297 " --> pdb=" O LYS T 293 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 337 removed outlier: 3.595A pdb=" N LEU T 333 " --> pdb=" O GLU T 329 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS T 336 " --> pdb=" O ALA T 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 359 through 363 removed outlier: 3.655A pdb=" N PHE T 363 " --> pdb=" O VAL T 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 359 through 363' Processing helix chain 'T' and resid 392 through 401 removed outlier: 4.456A pdb=" N TYR T 397 " --> pdb=" O GLU T 393 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR T 400 " --> pdb=" O ASP T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 403 through 407 Processing helix chain 'T' and resid 413 through 423 removed outlier: 3.636A pdb=" N GLN T 418 " --> pdb=" O PRO T 414 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE T 419 " --> pdb=" O VAL T 415 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE T 420 " --> pdb=" O VAL T 416 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR T 421 " --> pdb=" O GLU T 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 438 through 454 removed outlier: 3.682A pdb=" N ARG T 447 " --> pdb=" O ALA T 443 " (cutoff:3.500A) Processing helix chain 'T' and resid 476 through 488 removed outlier: 4.232A pdb=" N GLY T 480 " --> pdb=" O PRO T 476 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY T 483 " --> pdb=" O ILE T 479 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG T 484 " --> pdb=" O GLY T 480 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET T 486 " --> pdb=" O PHE T 482 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU T 487 " --> pdb=" O GLY T 483 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS T 488 " --> pdb=" O ARG T 484 " (cutoff:3.500A) Processing helix chain 'T' and resid 518 through 534 removed outlier: 3.544A pdb=" N GLU T 527 " --> pdb=" O THR T 523 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU T 530 " --> pdb=" O LYS T 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 36 removed outlier: 3.642A pdb=" N TRP A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 65 removed outlier: 3.595A pdb=" N TRP A 49 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 55 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 56 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN A 57 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 60 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 61 " --> pdb=" O MET A 58 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU A 64 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS A 65 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 101 through 115 Proline residue: A 106 - end of helix removed outlier: 3.590A pdb=" N TYR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 127 No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 129 through 138 removed outlier: 4.099A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'E' and resid 12 through 22 removed outlier: 3.805A pdb=" N TYR E 17 " --> pdb=" O SER E 14 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN E 19 " --> pdb=" O PHE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 51 removed outlier: 3.591A pdb=" N VAL E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 39 removed outlier: 4.100A pdb=" N ILE C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'S' and resid 92 through 94 Processing sheet with id= B, first strand: chain 'S' and resid 160 through 164 Processing sheet with id= C, first strand: chain 'S' and resid 206 through 208 removed outlier: 6.094A pdb=" N VAL S 185 " --> pdb=" O LYS S 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 383 through 385 Processing sheet with id= E, first strand: chain 'T' and resid 231 through 234 removed outlier: 3.736A pdb=" N GLY T 390 " --> pdb=" O ALA T 231 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY T 375 " --> pdb=" O TYR T 387 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU T 255 " --> pdb=" O LEU T 311 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU T 313 " --> pdb=" O LEU T 255 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU T 257 " --> pdb=" O LEU T 313 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR T 276 " --> pdb=" O ILE T 256 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER T 258 " --> pdb=" O THR T 276 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG T 278 " --> pdb=" O SER T 258 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 494 through 496 removed outlier: 3.953A pdb=" N VAL T 494 " --> pdb=" O ARG T 509 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG T 507 " --> pdb=" O VAL T 496 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 546 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: 2.13 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1649 1.32 - 1.45: 2352 1.45 - 1.58: 4978 1.58 - 1.70: 12 1.70 - 1.83: 84 Bond restraints: 9075 Sorted by residual: bond pdb=" C1' GE0 T 602 " pdb=" C2' GE0 T 602 " ideal model delta sigma weight residual 1.300 1.500 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C4' GE0 T 602 " pdb=" O4' GE0 T 602 " ideal model delta sigma weight residual 1.268 1.448 -0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C1' GE0 T 602 " pdb=" O4' GE0 T 602 " ideal model delta sigma weight residual 1.619 1.442 0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" CAE GE0 T 602 " pdb=" NAD GE0 T 602 " ideal model delta sigma weight residual 1.496 1.338 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" C6 GE0 T 602 " pdb=" N6 GE0 T 602 " ideal model delta sigma weight residual 1.459 1.324 0.135 2.00e-02 2.50e+03 4.54e+01 ... (remaining 9070 not shown) Histogram of bond angle deviations from ideal: 95.91 - 103.57: 144 103.57 - 111.22: 3434 111.22 - 118.87: 3767 118.87 - 126.52: 4824 126.52 - 134.17: 120 Bond angle restraints: 12289 Sorted by residual: angle pdb=" N VAL S 144 " pdb=" CA VAL S 144 " pdb=" C VAL S 144 " ideal model delta sigma weight residual 113.42 97.86 15.56 1.17e+00 7.31e-01 1.77e+02 angle pdb=" N LEU T 69 " pdb=" CA LEU T 69 " pdb=" C LEU T 69 " ideal model delta sigma weight residual 113.55 100.90 12.65 1.26e+00 6.30e-01 1.01e+02 angle pdb=" C HIS S 77 " pdb=" N PRO S 78 " pdb=" CA PRO S 78 " ideal model delta sigma weight residual 119.24 128.77 -9.53 1.04e+00 9.25e-01 8.40e+01 angle pdb=" C GLN T 300 " pdb=" N PRO T 301 " pdb=" CA PRO T 301 " ideal model delta sigma weight residual 119.84 130.56 -10.72 1.25e+00 6.40e-01 7.36e+01 angle pdb=" N TYR T 199 " pdb=" CA TYR T 199 " pdb=" C TYR T 199 " ideal model delta sigma weight residual 111.36 120.39 -9.03 1.09e+00 8.42e-01 6.87e+01 ... (remaining 12284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4753 17.20 - 34.39: 388 34.39 - 51.59: 205 51.59 - 68.79: 55 68.79 - 85.98: 5 Dihedral angle restraints: 5406 sinusoidal: 2173 harmonic: 3233 Sorted by residual: dihedral pdb=" CA LEU A 38 " pdb=" C LEU A 38 " pdb=" N SER A 39 " pdb=" CA SER A 39 " ideal model delta harmonic sigma weight residual -180.00 -138.52 -41.48 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA LEU A 142 " pdb=" C LEU A 142 " pdb=" N HIS A 143 " pdb=" CA HIS A 143 " ideal model delta harmonic sigma weight residual -180.00 -139.84 -40.16 0 5.00e+00 4.00e-02 6.45e+01 dihedral pdb=" C PHE S 394 " pdb=" N PHE S 394 " pdb=" CA PHE S 394 " pdb=" CB PHE S 394 " ideal model delta harmonic sigma weight residual -122.60 -139.75 17.15 0 2.50e+00 1.60e-01 4.70e+01 ... (remaining 5403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 1238 0.138 - 0.277: 118 0.277 - 0.415: 16 0.415 - 0.553: 2 0.553 - 0.692: 1 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CA PHE S 394 " pdb=" N PHE S 394 " pdb=" C PHE S 394 " pdb=" CB PHE S 394 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ASN T 120 " pdb=" N ASN T 120 " pdb=" C ASN T 120 " pdb=" CB ASN T 120 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA TYR T 235 " pdb=" N TYR T 235 " pdb=" C TYR T 235 " pdb=" CB TYR T 235 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1372 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG T 305 " 0.047 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO T 306 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO T 306 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO T 306 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 45 " 0.047 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO A 46 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 46 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 46 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE S 61 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C ILE S 61 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE S 61 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU S 62 " -0.016 2.00e-02 2.50e+03 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 1.00 - 1.78: 8 1.78 - 2.56: 85 2.56 - 3.34: 10255 3.34 - 4.12: 20021 4.12 - 4.90: 38230 Warning: very small nonbonded interaction distances. Nonbonded interactions: 68599 Sorted by model distance: nonbonded pdb=" OD1 ASP T 344 " pdb=" CE MET T 374 " model vdw 0.997 3.460 nonbonded pdb=" OD2 ASP S 188 " pdb=" OH TYR S 248 " model vdw 1.295 2.440 nonbonded pdb=" CG1 VAL T 195 " pdb=" OE1 GLU T 417 " model vdw 1.387 3.460 nonbonded pdb=" OE1 GLU T 119 " pdb=" O PHE A 72 " model vdw 1.491 3.040 nonbonded pdb=" O LYS T 194 " pdb=" OE2 GLU T 197 " model vdw 1.636 3.040 ... (remaining 68594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.80 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 4.390 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 26.440 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.012 0.200 9075 Z= 0.825 Angle : 1.506 17.689 12289 Z= 0.882 Chirality : 0.090 0.692 1375 Planarity : 0.008 0.072 1550 Dihedral : 16.827 85.983 3336 Min Nonbonded Distance : 0.997 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.68 % Favored : 88.60 % Rotamer Outliers : 13.06 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -5.50 (0.19), residues: 1105 helix: -4.40 (0.13), residues: 474 sheet: -2.54 (0.52), residues: 92 loop : -3.07 (0.22), residues: 539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 179 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 65 residues processed: 275 average time/residue: 0.2803 time to fit residues: 100.1801 Evaluate side-chains 172 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 107 time to evaluate : 1.015 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 65 outliers final: 1 residues processed: 65 average time/residue: 0.1542 time to fit residues: 16.3364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 83 ASN S 114 ASN S 211 HIS S 224 GLN S 327 HIS S 395 HIS T 120 ASN T 242 ASN T 262 ASN T 263 HIS T 284 ASN T 418 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN E 38 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9075 Z= 0.239 Angle : 0.718 11.358 12289 Z= 0.364 Chirality : 0.047 0.194 1375 Planarity : 0.006 0.059 1550 Dihedral : 8.279 83.743 1246 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.21), residues: 1105 helix: -2.98 (0.19), residues: 456 sheet: -2.08 (0.54), residues: 96 loop : -2.79 (0.23), residues: 553 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 0.956 Fit side-chains outliers start: 24 outliers final: 6 residues processed: 139 average time/residue: 0.2139 time to fit residues: 41.5186 Evaluate side-chains 101 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1367 time to fit residues: 2.6450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 107 ASN S 327 HIS A 18 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 9075 Z= 0.295 Angle : 0.684 9.205 12289 Z= 0.347 Chirality : 0.047 0.188 1375 Planarity : 0.005 0.054 1550 Dihedral : 7.882 83.804 1246 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer Outliers : 3.72 % 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: -3.58 (0.23), residues: 1105 helix: -2.24 (0.21), residues: 465 sheet: -1.92 (0.56), residues: 96 loop : -2.55 (0.24), residues: 544 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.117 Fit side-chains outliers start: 35 outliers final: 17 residues processed: 134 average time/residue: 0.2179 time to fit residues: 41.3727 Evaluate side-chains 114 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0949 time to fit residues: 4.2975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 327 HIS ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 9075 Z= 0.312 Angle : 0.666 10.225 12289 Z= 0.336 Chirality : 0.047 0.178 1375 Planarity : 0.005 0.053 1550 Dihedral : 7.756 81.699 1246 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.33 % Favored : 91.58 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.23), residues: 1105 helix: -1.84 (0.22), residues: 478 sheet: -2.14 (0.58), residues: 82 loop : -2.47 (0.25), residues: 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.079 Fit side-chains outliers start: 19 outliers final: 5 residues processed: 119 average time/residue: 0.2127 time to fit residues: 35.6464 Evaluate side-chains 98 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0942 time to fit residues: 2.3049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 9075 Z= 0.240 Angle : 0.614 8.625 12289 Z= 0.310 Chirality : 0.045 0.176 1375 Planarity : 0.004 0.051 1550 Dihedral : 7.411 78.562 1246 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.42 % Favored : 92.49 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.24), residues: 1105 helix: -1.52 (0.23), residues: 479 sheet: -2.03 (0.58), residues: 82 loop : -2.36 (0.25), residues: 544 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.997 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 110 average time/residue: 0.2139 time to fit residues: 33.5687 Evaluate side-chains 101 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0882 time to fit residues: 2.8561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 9.9990 chunk 95 optimal weight: 0.0570 chunk 21 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 9075 Z= 0.151 Angle : 0.576 10.305 12289 Z= 0.288 Chirality : 0.043 0.176 1375 Planarity : 0.004 0.050 1550 Dihedral : 6.929 73.325 1246 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.79 % Favored : 93.12 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.25), residues: 1105 helix: -1.20 (0.24), residues: 480 sheet: -1.92 (0.58), residues: 82 loop : -2.20 (0.25), residues: 543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.018 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 116 average time/residue: 0.2165 time to fit residues: 35.4731 Evaluate side-chains 102 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0869 time to fit residues: 2.1508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.0000 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 107 ASN S 395 HIS T 282 HIS ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9075 Z= 0.143 Angle : 0.565 9.163 12289 Z= 0.285 Chirality : 0.043 0.191 1375 Planarity : 0.004 0.044 1550 Dihedral : 6.556 69.319 1246 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.15 % Favored : 93.76 % Rotamer Outliers : 0.53 % 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: -2.29 (0.25), residues: 1105 helix: -0.87 (0.25), residues: 475 sheet: -1.62 (0.60), residues: 81 loop : -2.10 (0.25), residues: 549 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.118 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 106 average time/residue: 0.2302 time to fit residues: 34.9012 Evaluate side-chains 97 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0951 time to fit residues: 1.8679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 107 ASN T 245 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9075 Z= 0.175 Angle : 0.567 8.190 12289 Z= 0.284 Chirality : 0.043 0.177 1375 Planarity : 0.004 0.043 1550 Dihedral : 6.460 69.065 1246 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.79 % Favored : 93.12 % Rotamer Outliers : 1.17 % 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: -2.19 (0.25), residues: 1105 helix: -0.75 (0.25), residues: 477 sheet: -1.52 (0.60), residues: 81 loop : -2.08 (0.26), residues: 547 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.029 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 106 average time/residue: 0.2321 time to fit residues: 34.7720 Evaluate side-chains 100 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0926 time to fit residues: 2.2403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.0370 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.0060 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 9075 Z= 0.137 Angle : 0.556 12.712 12289 Z= 0.277 Chirality : 0.043 0.190 1375 Planarity : 0.004 0.044 1550 Dihedral : 6.236 63.902 1246 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.79 % Favored : 94.12 % Rotamer Outliers : 0.53 % 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 (0.25), residues: 1105 helix: -0.49 (0.25), residues: 470 sheet: -1.34 (0.65), residues: 71 loop : -2.01 (0.25), residues: 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.105 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 0.2145 time to fit residues: 33.2250 Evaluate side-chains 96 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0929 time to fit residues: 1.8610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 0.0980 chunk 9 optimal weight: 0.4980 chunk 67 optimal weight: 0.3980 chunk 53 optimal weight: 0.0020 chunk 69 optimal weight: 0.3980 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 133 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9075 Z= 0.133 Angle : 0.545 8.346 12289 Z= 0.272 Chirality : 0.042 0.175 1375 Planarity : 0.004 0.047 1550 Dihedral : 6.046 59.636 1246 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.97 % Favored : 93.94 % Rotamer Outliers : 0.32 % 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: -1.77 (0.26), residues: 1105 helix: -0.34 (0.26), residues: 470 sheet: -1.29 (0.65), residues: 71 loop : -1.91 (0.25), residues: 564 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.118 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 104 average time/residue: 0.2223 time to fit residues: 32.8810 Evaluate side-chains 95 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.0370 chunk 63 optimal weight: 0.8980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 306 ASN T 133 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111645 restraints weight = 12099.256| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.89 r_work: 0.3158 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 9075 Z= 0.138 Angle : 0.551 10.131 12289 Z= 0.275 Chirality : 0.043 0.175 1375 Planarity : 0.004 0.048 1550 Dihedral : 5.967 59.031 1246 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.88 % Favored : 94.03 % Rotamer Outliers : 0.42 % 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: -1.69 (0.26), residues: 1105 helix: -0.27 (0.25), residues: 473 sheet: -1.19 (0.65), residues: 71 loop : -1.89 (0.26), residues: 561 =============================================================================== Job complete usr+sys time: 2117.69 seconds wall clock time: 39 minutes 3.22 seconds (2343.22 seconds total)