Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 22:38:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/08_2023/6vwg_21415_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/08_2023/6vwg_21415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/08_2023/6vwg_21415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/08_2023/6vwg_21415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/08_2023/6vwg_21415_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwg_21415/08_2023/6vwg_21415_trim.pdb" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4078 2.51 5 N 1115 2.21 5 O 1224 1.98 5 H 6282 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 336": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A ARG 450": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "B ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B ASP 461": "OD1" <-> "OD2" Residue "B ARG 481": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 562": "OD1" <-> "OD2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B ARG 689": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 12751 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6916 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 4980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4980 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Chain: "I" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 799 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.43, per 1000 atoms: 0.43 Number of scatterers: 12751 At special positions: 0 Unit cell: (76.32, 108.12, 104.94, 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 52 16.00 O 1224 8.00 N 1115 7.00 C 4078 6.00 H 6282 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.02 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.04 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 323 " distance=2.02 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 458 " distance=2.03 Simple disulfide: pdb=" SG CYS I 9 " - pdb=" SG CYS I 47 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 60 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 21 " " NAG A1002 " - " ASN A 387 " " NAG A1003 " - " ASN A 105 " " NAG B1001 " - " ASN B 504 " Time building additional restraints: 10.15 Conformation dependent library (CDL) restraints added in 993.7 milliseconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 23.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.596A pdb=" N LYS A 17 " --> pdb=" O GLN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.255A pdb=" N LEU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 4.007A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 149 removed outlier: 4.344A pdb=" N GLY A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 195 through 199 removed outlier: 4.053A pdb=" N GLU A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 313 through 319 removed outlier: 3.849A pdb=" N MET A 319 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 348 removed outlier: 4.991A pdb=" N GLU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.510A pdb=" N HIS A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 431 removed outlier: 3.813A pdb=" N ILE A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.582A pdb=" N VAL A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 321 removed outlier: 3.836A pdb=" N GLN B 318 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET B 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 348 removed outlier: 3.728A pdb=" N GLU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 428 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 486 through 488 No H-bonds generated for 'chain 'B' and resid 486 through 488' Processing helix chain 'B' and resid 558 through 563 removed outlier: 4.026A pdb=" N ASP B 562 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 701 removed outlier: 4.186A pdb=" N LYS B 683 " --> pdb=" O LYS B 679 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE B 692 " --> pdb=" O TYR B 688 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 22 removed outlier: 3.592A pdb=" N VAL I 14 " --> pdb=" O GLY I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 25 No H-bonds generated for 'chain 'I' and resid 23 through 25' Processing helix chain 'I' and resid 41 through 47 Processing helix chain 'I' and resid 52 through 57 removed outlier: 3.543A pdb=" N GLU I 57 " --> pdb=" O LEU I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9 removed outlier: 6.756A pdb=" N ILE A 7 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N LEU A 32 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 29 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE A 58 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 209 removed outlier: 3.811A pdb=" N ALA A 220 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N SER A 208 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N CYS A 218 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 241 removed outlier: 4.175A pdb=" N ARG A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA8, first strand: chain 'A' and resid 308 through 311 removed outlier: 6.399A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG A 361 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 332 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 358 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU A 393 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE A 360 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR A 388 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TYR A 417 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A 390 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ALA A 419 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 392 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AB1, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.589A pdb=" N LEU B 331 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 330 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ARG B 361 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 332 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 358 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU B 393 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 360 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N TYR B 417 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR B 391 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA B 419 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU B 393 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AB3, first strand: chain 'B' and resid 465 through 470 Processing sheet with id=AB4, first strand: chain 'B' and resid 520 through 524 removed outlier: 3.514A pdb=" N SER B 492 " --> pdb=" O VAL B 554 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 10.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6281 1.03 - 1.23: 3 1.23 - 1.42: 2776 1.42 - 1.62: 3750 1.62 - 1.82: 67 Bond restraints: 12877 Sorted by residual: bond pdb=" C1 NAG A1002 " pdb=" O5 NAG A1002 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" N SER I 5 " pdb=" CA SER I 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" N SER I 5 " pdb=" H SER I 5 " ideal model delta sigma weight residual 0.860 0.888 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 12872 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.20: 112 105.20 - 112.40: 14450 112.40 - 119.60: 3544 119.60 - 126.80: 5003 126.80 - 134.00: 77 Bond angle restraints: 23186 Sorted by residual: angle pdb=" N GLU A 305 " pdb=" CA GLU A 305 " pdb=" C GLU A 305 " ideal model delta sigma weight residual 110.80 102.62 8.18 2.13e+00 2.20e-01 1.47e+01 angle pdb=" N PHE A 45 " pdb=" CA PHE A 45 " pdb=" C PHE A 45 " ideal model delta sigma weight residual 108.39 114.26 -5.87 2.10e+00 2.27e-01 7.82e+00 angle pdb=" N ARG A 336 " pdb=" CA ARG A 336 " pdb=" C ARG A 336 " ideal model delta sigma weight residual 108.32 112.89 -4.57 1.64e+00 3.72e-01 7.78e+00 angle pdb=" N GLU A 304 " pdb=" CA GLU A 304 " pdb=" C GLU A 304 " ideal model delta sigma weight residual 110.50 114.29 -3.79 1.41e+00 5.03e-01 7.23e+00 angle pdb=" N PHE B 420 " pdb=" CA PHE B 420 " pdb=" C PHE B 420 " ideal model delta sigma weight residual 110.80 116.39 -5.59 2.13e+00 2.20e-01 6.89e+00 ... (remaining 23181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4688 17.90 - 35.80: 367 35.80 - 53.70: 80 53.70 - 71.59: 62 71.59 - 89.49: 9 Dihedral angle restraints: 5206 sinusoidal: 2461 harmonic: 2745 Sorted by residual: dihedral pdb=" CB CYS A 189 " pdb=" SG CYS A 189 " pdb=" SG CYS A 200 " pdb=" CB CYS A 200 " ideal model delta sinusoidal sigma weight residual 93.00 155.18 -62.18 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS A 234 " pdb=" SG CYS A 234 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual -86.00 -142.75 56.75 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CA GLU A 305 " pdb=" C GLU A 305 " pdb=" N LYS A 306 " pdb=" CA LYS A 306 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 5203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 533 0.037 - 0.075: 307 0.075 - 0.112: 130 0.112 - 0.149: 17 0.149 - 0.187: 4 Chirality restraints: 991 Sorted by residual: chirality pdb=" CA ARG A 104 " pdb=" N ARG A 104 " pdb=" C ARG A 104 " pdb=" CB ARG A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA HIS A 362 " pdb=" N HIS A 362 " pdb=" C HIS A 362 " pdb=" CB HIS A 362 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" C2 NAG A1002 " pdb=" C1 NAG A1002 " pdb=" C3 NAG A1002 " pdb=" N2 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.49 -2.34 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 988 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 174 " 0.016 9.50e-02 1.11e+02 4.99e-02 5.54e+01 pdb=" NE ARG A 174 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 174 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 174 " -0.091 2.00e-02 2.50e+03 pdb=" NH2 ARG A 174 " -0.006 2.00e-02 2.50e+03 pdb="HH11 ARG A 174 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 174 " 0.092 2.00e-02 2.50e+03 pdb="HH21 ARG A 174 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 174 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 112 " -0.123 9.50e-02 1.11e+02 5.74e-02 3.83e+01 pdb=" NE ARG A 112 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 112 " -0.076 2.00e-02 2.50e+03 pdb=" NH1 ARG A 112 " 0.073 2.00e-02 2.50e+03 pdb=" NH2 ARG A 112 " 0.046 2.00e-02 2.50e+03 pdb="HH11 ARG A 112 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG A 112 " -0.018 2.00e-02 2.50e+03 pdb="HH21 ARG A 112 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 112 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 680 " -0.036 2.00e-02 2.50e+03 4.39e-02 2.89e+01 pdb=" CD GLN B 680 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN B 680 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN B 680 " 0.070 2.00e-02 2.50e+03 pdb="HE21 GLN B 680 " 0.002 2.00e-02 2.50e+03 pdb="HE22 GLN B 680 " -0.067 2.00e-02 2.50e+03 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 549 2.15 - 2.76: 24376 2.76 - 3.37: 34633 3.37 - 3.99: 44831 3.99 - 4.60: 71369 Nonbonded interactions: 175758 Sorted by model distance: nonbonded pdb=" OE2 GLU B 433 " pdb="HE21 GLN B 442 " model vdw 1.535 1.850 nonbonded pdb=" O GLY A 437 " pdb=" HG1 THR A 438 " model vdw 1.560 1.850 nonbonded pdb=" O LEU B 424 " pdb="HD22 ASN B 452 " model vdw 1.565 1.850 nonbonded pdb=" HZ1 LYS B 498 " pdb=" OD2 ASP B 509 " model vdw 1.566 1.850 nonbonded pdb=" HG SER B 363 " pdb=" OD1 ASN B 395 " model vdw 1.567 1.850 ... (remaining 175753 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=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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 14.220 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 41.700 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.060 6595 Z= 0.438 Angle : 0.890 8.179 8908 Z= 0.509 Chirality : 0.051 0.187 991 Planarity : 0.006 0.068 1140 Dihedral : 14.655 89.492 2440 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.78 (0.28), residues: 782 helix: -3.47 (0.35), residues: 103 sheet: -0.92 (0.52), residues: 111 loop : -1.84 (0.25), residues: 568 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 145 average time/residue: 0.4856 time to fit residues: 88.9438 Evaluate side-chains 73 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 1.102 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1631 time to fit residues: 2.4902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 223 HIS A 333 ASN A 451 ASN B 396 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 6595 Z= 0.239 Angle : 0.680 5.313 8908 Z= 0.373 Chirality : 0.044 0.149 991 Planarity : 0.004 0.038 1140 Dihedral : 7.754 32.943 877 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -2.45 (0.29), residues: 782 helix: -2.61 (0.43), residues: 104 sheet: -1.03 (0.50), residues: 121 loop : -1.66 (0.26), residues: 557 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 91 average time/residue: 0.4555 time to fit residues: 53.8716 Evaluate side-chains 80 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 1.049 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.1637 time to fit residues: 3.2928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 6595 Z= 0.373 Angle : 0.687 7.125 8908 Z= 0.371 Chirality : 0.045 0.163 991 Planarity : 0.004 0.035 1140 Dihedral : 7.335 32.429 877 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.49 (0.28), residues: 782 helix: -2.20 (0.47), residues: 97 sheet: -1.58 (0.47), residues: 114 loop : -1.67 (0.25), residues: 571 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 93 average time/residue: 0.3899 time to fit residues: 48.9698 Evaluate side-chains 74 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 1.007 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1660 time to fit residues: 2.7342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 6595 Z= 0.234 Angle : 0.599 6.755 8908 Z= 0.324 Chirality : 0.043 0.142 991 Planarity : 0.003 0.030 1140 Dihedral : 6.885 30.683 877 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.52 (0.28), residues: 782 helix: -1.98 (0.49), residues: 99 sheet: -1.62 (0.48), residues: 104 loop : -1.74 (0.25), residues: 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 84 average time/residue: 0.3624 time to fit residues: 41.9439 Evaluate side-chains 77 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 1.082 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1603 time to fit residues: 2.8049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 6595 Z= 0.361 Angle : 0.656 7.150 8908 Z= 0.352 Chirality : 0.044 0.150 991 Planarity : 0.004 0.039 1140 Dihedral : 6.859 30.564 877 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.28), residues: 782 helix: -2.08 (0.47), residues: 104 sheet: -2.03 (0.45), residues: 109 loop : -1.99 (0.25), residues: 569 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 84 average time/residue: 0.3517 time to fit residues: 41.7781 Evaluate side-chains 75 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.985 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1613 time to fit residues: 3.5803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 6595 Z= 0.255 Angle : 0.597 6.960 8908 Z= 0.320 Chirality : 0.043 0.143 991 Planarity : 0.003 0.034 1140 Dihedral : 6.609 30.155 877 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.83 (0.28), residues: 782 helix: -1.94 (0.47), residues: 104 sheet: -1.91 (0.46), residues: 109 loop : -1.99 (0.25), residues: 569 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 78 average time/residue: 0.3464 time to fit residues: 37.9135 Evaluate side-chains 71 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 1.049 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1690 time to fit residues: 2.2903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 6595 Z= 0.227 Angle : 0.582 8.116 8908 Z= 0.311 Chirality : 0.043 0.147 991 Planarity : 0.003 0.035 1140 Dihedral : 6.391 29.789 877 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.75 (0.28), residues: 782 helix: -1.82 (0.47), residues: 104 sheet: -1.71 (0.49), residues: 104 loop : -1.99 (0.25), residues: 574 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 0.3735 time to fit residues: 39.0699 Evaluate side-chains 72 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 1.178 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1840 time to fit residues: 1.9874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 6595 Z= 0.257 Angle : 0.594 8.313 8908 Z= 0.317 Chirality : 0.043 0.146 991 Planarity : 0.003 0.035 1140 Dihedral : 6.354 29.607 877 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.67 (0.28), residues: 782 helix: -1.58 (0.50), residues: 98 sheet: -1.71 (0.49), residues: 104 loop : -1.96 (0.25), residues: 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 77 average time/residue: 0.3807 time to fit residues: 40.4675 Evaluate side-chains 75 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.030 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1750 time to fit residues: 1.9097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 6595 Z= 0.175 Angle : 0.558 8.918 8908 Z= 0.297 Chirality : 0.042 0.145 991 Planarity : 0.003 0.035 1140 Dihedral : 6.115 29.306 877 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.54 (0.28), residues: 782 helix: -1.38 (0.51), residues: 98 sheet: -1.49 (0.50), residues: 104 loop : -1.91 (0.25), residues: 580 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 84 average time/residue: 0.4040 time to fit residues: 46.6745 Evaluate side-chains 75 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.041 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1871 time to fit residues: 2.0127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 57 optimal weight: 0.0000 chunk 9 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6595 Z= 0.175 Angle : 0.559 9.301 8908 Z= 0.296 Chirality : 0.042 0.143 991 Planarity : 0.003 0.035 1140 Dihedral : 6.015 29.055 877 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.43 (0.29), residues: 782 helix: -1.25 (0.52), residues: 92 sheet: -1.45 (0.48), residues: 114 loop : -1.83 (0.25), residues: 576 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 84 average time/residue: 0.3509 time to fit residues: 41.3570 Evaluate side-chains 75 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.147 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1810 time to fit residues: 1.9430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.125911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.106933 restraints weight = 32781.626| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.75 r_work: 0.3574 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6595 Z= 0.214 Angle : 0.576 9.003 8908 Z= 0.306 Chirality : 0.042 0.139 991 Planarity : 0.003 0.037 1140 Dihedral : 6.027 29.063 877 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.49 (0.28), residues: 782 helix: -1.29 (0.52), residues: 92 sheet: -1.45 (0.51), residues: 104 loop : -1.89 (0.25), residues: 586 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3535.85 seconds wall clock time: 63 minutes 6.89 seconds (3786.89 seconds total)