Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 22:43:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwi_21417/08_2023/6vwi_21417_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwi_21417/08_2023/6vwi_21417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwi_21417/08_2023/6vwi_21417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwi_21417/08_2023/6vwi_21417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwi_21417/08_2023/6vwi_21417_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwi_21417/08_2023/6vwi_21417_trim.pdb" } resolution = 3.7 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= 0.032 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 6283 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 ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A ASP 39": "OD1" <-> "OD2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 150": "OD1" <-> "OD2" 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 ASP 213": "OD1" <-> "OD2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 304": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A ARG 336": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ASP 403": "OD1" <-> "OD2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 450": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 376": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B GLU 434": "OE1" <-> "OE2" Residue "B ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 481": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 483": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 486": "OD1" <-> "OD2" Residue "B TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 560": "OE1" <-> "OE2" Residue "B ARG 565": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 678": "OE1" <-> "OE2" Residue "B GLU 682": "OE1" <-> "OE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B GLU 687": "OE1" <-> "OE2" Residue "B ARG 689": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 693": "OE1" <-> "OE2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 12752 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: 4981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4981 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: 5.81, per 1000 atoms: 0.46 Number of scatterers: 12752 At special positions: 0 Unit cell: (78.44, 110.24, 107.06, 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 6283 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=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.02 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.02 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=2.03 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=2.02 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: 9.95 Conformation dependent library (CDL) restraints added in 972.1 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: 23 helices and 18 sheets defined 21.2% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.791A pdb=" N LYS A 17 " --> pdb=" O GLN A 14 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.681A pdb=" N TYR A 43 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.798A pdb=" N CYS A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 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 253 Processing helix chain 'A' and resid 313 through 319 removed outlier: 3.661A pdb=" N MET A 319 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 removed outlier: 4.004A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.908A pdb=" N GLU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.747A pdb=" N ILE B 429 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 447 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 560 through 564 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 683 through 701 removed outlier: 5.028A pdb=" N ARG B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N PHE B 692 " --> pdb=" O TYR B 688 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 22 Processing helix chain 'I' and resid 41 through 47 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.520A pdb=" N ILE A 76 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9 removed outlier: 6.819A pdb=" N ILE A 7 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LEU A 32 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 29 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE A 58 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 111 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 140 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE A 113 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 165 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.561A pdb=" N THR A 177 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 209 removed outlier: 3.548A pdb=" N ALA A 220 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER A 208 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N CYS A 218 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA8, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AB1, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB2, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AB3, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.650A pdb=" N LEU A 331 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 358 through 361 removed outlier: 6.659A pdb=" N VAL A 358 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LEU A 393 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 360 " --> pdb=" O LEU A 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 301 through 311 removed outlier: 5.991A pdb=" N ILE B 325 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU B 303 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS B 327 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU B 305 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ASN B 329 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS B 307 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU B 331 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 309 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 301 through 311 removed outlier: 5.991A pdb=" N ILE B 325 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU B 303 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS B 327 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU B 305 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ASN B 329 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS B 307 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU B 331 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 309 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N LYS B 359 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 330 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ARG B 361 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE B 332 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TYR B 417 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR B 391 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ALA B 419 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 393 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 461 through 463 removed outlier: 5.894A pdb=" N ASP B 461 " --> pdb=" O LYS B 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 465 through 470 removed outlier: 3.694A pdb=" N SER B 467 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 520 through 524 removed outlier: 3.845A pdb=" N SER B 492 " --> pdb=" O VAL B 554 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 315 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: 4.33 Time building geometry restraints manager: 10.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6282 1.03 - 1.23: 150 1.23 - 1.43: 2645 1.43 - 1.63: 3734 1.63 - 1.83: 67 Bond restraints: 12878 Sorted by residual: bond pdb=" C1 NAG A1002 " pdb=" O5 NAG A1002 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C1 NAG A1003 " pdb=" C2 NAG A1003 " ideal model delta sigma weight residual 1.532 1.486 0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.85e+00 bond pdb=" N SER I 5 " pdb=" CA SER I 5 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 12873 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.04: 126 106.04 - 113.06: 14840 113.06 - 120.08: 4110 120.08 - 127.11: 4045 127.11 - 134.13: 67 Bond angle restraints: 23188 Sorted by residual: angle pdb=" N LYS A 373 " pdb=" CA LYS A 373 " pdb=" C LYS A 373 " ideal model delta sigma weight residual 111.11 115.51 -4.40 1.20e+00 6.94e-01 1.35e+01 angle pdb=" N ARG B 407 " pdb=" CA ARG B 407 " pdb=" C ARG B 407 " ideal model delta sigma weight residual 108.69 114.45 -5.76 1.77e+00 3.19e-01 1.06e+01 angle pdb=" CA TRP B 544 " pdb=" CB TRP B 544 " pdb=" CG TRP B 544 " ideal model delta sigma weight residual 113.60 119.04 -5.44 1.90e+00 2.77e-01 8.19e+00 angle pdb=" N ASN A 11 " pdb=" CA ASN A 11 " pdb=" C ASN A 11 " ideal model delta sigma weight residual 110.80 116.86 -6.06 2.13e+00 2.20e-01 8.09e+00 angle pdb=" N LEU B 366 " pdb=" CA LEU B 366 " pdb=" C LEU B 366 " ideal model delta sigma weight residual 107.99 112.67 -4.68 1.77e+00 3.19e-01 6.99e+00 ... (remaining 23183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4680 17.65 - 35.30: 371 35.30 - 52.95: 72 52.95 - 70.60: 72 70.60 - 88.25: 12 Dihedral angle restraints: 5207 sinusoidal: 2461 harmonic: 2746 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 181 " pdb=" CB CYS A 181 " ideal model delta sinusoidal sigma weight residual -86.00 -164.87 78.87 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CA ASN B 374 " pdb=" C ASN B 374 " pdb=" N LEU B 375 " pdb=" CA LEU B 375 " ideal model delta harmonic sigma weight residual -180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CB CYS A 252 " pdb=" SG CYS A 252 " pdb=" SG CYS A 273 " pdb=" CB CYS A 273 " ideal model delta sinusoidal sigma weight residual -86.00 -135.20 49.20 1 1.00e+01 1.00e-02 3.33e+01 ... (remaining 5204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 525 0.035 - 0.069: 293 0.069 - 0.104: 126 0.104 - 0.138: 42 0.138 - 0.173: 5 Chirality restraints: 991 Sorted by residual: chirality pdb=" CA CYS I 46 " pdb=" N CYS I 46 " pdb=" C CYS I 46 " pdb=" CB CYS I 46 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-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 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" C1 NAG A1003 " pdb=" ND2 ASN A 105 " pdb=" C2 NAG A1003 " pdb=" O5 NAG A1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 988 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 395 " 0.055 2.00e-02 2.50e+03 6.42e-02 6.19e+01 pdb=" CG ASN A 395 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A 395 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 395 " -0.094 2.00e-02 2.50e+03 pdb="HD21 ASN A 395 " -0.003 2.00e-02 2.50e+03 pdb="HD22 ASN A 395 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 336 " -0.150 9.50e-02 1.11e+02 6.80e-02 5.02e+01 pdb=" NE ARG A 336 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG A 336 " 0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG A 336 " -0.067 2.00e-02 2.50e+03 pdb=" NH2 ARG A 336 " 0.025 2.00e-02 2.50e+03 pdb="HH11 ARG A 336 " -0.027 2.00e-02 2.50e+03 pdb="HH12 ARG A 336 " 0.075 2.00e-02 2.50e+03 pdb="HH21 ARG A 336 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 336 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 395 " -0.041 2.00e-02 2.50e+03 5.08e-02 3.86e+01 pdb=" CG ASN B 395 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 395 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 395 " 0.080 2.00e-02 2.50e+03 pdb="HD21 ASN B 395 " 0.001 2.00e-02 2.50e+03 pdb="HD22 ASN B 395 " -0.077 2.00e-02 2.50e+03 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 494 2.13 - 2.75: 23964 2.75 - 3.37: 34936 3.37 - 3.98: 44530 3.98 - 4.60: 70137 Nonbonded interactions: 174061 Sorted by model distance: nonbonded pdb=" HG1 THR A 195 " pdb=" O CYS A 209 " model vdw 1.513 1.850 nonbonded pdb="HH11 ARG A 174 " pdb=" OE1 GLN A 182 " model vdw 1.546 1.850 nonbonded pdb=" H CYS I 9 " pdb=" OE2 GLU I 12 " model vdw 1.548 1.850 nonbonded pdb=" O ALA A 61 " pdb="HD21 ASN A 94 " model vdw 1.572 1.850 nonbonded pdb=" HZ2 LYS A 164 " pdb=" OH TYR A 171 " model vdw 1.597 1.850 ... (remaining 174056 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 13.990 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 40.920 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 0.053 6595 Z= 0.440 Angle : 0.878 6.059 8908 Z= 0.498 Chirality : 0.051 0.173 991 Planarity : 0.008 0.108 1140 Dihedral : 14.896 88.250 2440 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.44 (0.28), residues: 782 helix: -3.51 (0.33), residues: 101 sheet: -0.76 (0.46), residues: 118 loop : -1.53 (0.26), residues: 563 *********************** 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 149 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.044 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 148 average time/residue: 0.4621 time to fit residues: 86.6171 Evaluate side-chains 77 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1490 time to fit residues: 2.1754 ------------------------------------------------------------------------------- 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: 1.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 333 ASN B 374 ASN B 387 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 6595 Z= 0.219 Angle : 0.678 6.750 8908 Z= 0.370 Chirality : 0.047 0.165 991 Planarity : 0.004 0.033 1140 Dihedral : 7.662 28.043 877 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.81 (0.29), residues: 782 helix: -2.14 (0.46), residues: 108 sheet: -0.92 (0.44), residues: 125 loop : -1.09 (0.27), residues: 549 *********************** 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 103 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.131 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 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: 11 residues processed: 98 average time/residue: 0.4163 time to fit residues: 54.0160 Evaluate side-chains 81 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 1.058 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2039 time to fit residues: 4.8721 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.0050 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6595 Z= 0.175 Angle : 0.586 5.976 8908 Z= 0.316 Chirality : 0.045 0.154 991 Planarity : 0.003 0.025 1140 Dihedral : 6.543 21.160 877 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % 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: -1.60 (0.30), residues: 782 helix: -1.51 (0.50), residues: 108 sheet: -1.14 (0.43), residues: 115 loop : -0.97 (0.27), residues: 559 *********************** 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 85 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 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 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: 84 average time/residue: 0.3643 time to fit residues: 41.8444 Evaluate side-chains 70 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1408 time to fit residues: 2.1026 ------------------------------------------------------------------------------- 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: 0.8980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.0030 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4181 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= 0.197 Angle : 0.583 5.840 8908 Z= 0.315 Chirality : 0.045 0.188 991 Planarity : 0.003 0.028 1140 Dihedral : 6.203 22.469 877 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer Outliers : 1.54 % 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: -1.66 (0.30), residues: 782 helix: -1.47 (0.49), residues: 107 sheet: -1.31 (0.43), residues: 115 loop : -1.00 (0.28), residues: 560 *********************** 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 79 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 1.047 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: 11 outliers final: 4 residues processed: 75 average time/residue: 0.3938 time to fit residues: 39.8477 Evaluate side-chains 67 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 1.026 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1565 time to fit residues: 2.4006 ------------------------------------------------------------------------------- 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: 1.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.035 6595 Z= 0.379 Angle : 0.694 5.846 8908 Z= 0.372 Chirality : 0.048 0.194 991 Planarity : 0.005 0.044 1140 Dihedral : 6.658 22.796 877 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer Outliers : 2.53 % 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: -2.20 (0.29), residues: 782 helix: -1.72 (0.47), residues: 95 sheet: -1.87 (0.44), residues: 102 loop : -1.42 (0.26), residues: 585 *********************** 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 83 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 1.048 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: 18 outliers final: 8 residues processed: 76 average time/residue: 0.3675 time to fit residues: 38.6751 Evaluate side-chains 68 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.965 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1755 time to fit residues: 3.5450 ------------------------------------------------------------------------------- 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: 0.0170 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 383 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 6595 Z= 0.144 Angle : 0.552 5.060 8908 Z= 0.294 Chirality : 0.045 0.153 991 Planarity : 0.003 0.040 1140 Dihedral : 5.846 19.855 877 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer Outliers : 1.12 % 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: -1.94 (0.29), residues: 782 helix: -1.52 (0.47), residues: 107 sheet: -1.67 (0.43), residues: 113 loop : -1.20 (0.27), residues: 562 *********************** 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 73 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 1.066 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: 8 outliers final: 4 residues processed: 70 average time/residue: 0.3811 time to fit residues: 36.5587 Evaluate side-chains 64 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1528 time to fit residues: 2.4503 ------------------------------------------------------------------------------- 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: 0.0070 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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: 0.7405 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6595 Z= 0.191 Angle : 0.561 8.531 8908 Z= 0.298 Chirality : 0.045 0.150 991 Planarity : 0.003 0.044 1140 Dihedral : 5.762 21.701 877 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.72 % Favored : 90.15 % 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: -1.88 (0.29), residues: 782 helix: -1.36 (0.48), residues: 107 sheet: -1.59 (0.45), residues: 107 loop : -1.20 (0.27), residues: 568 *********************** 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 63 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.065 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: 4 outliers final: 2 residues processed: 62 average time/residue: 0.3823 time to fit residues: 32.4574 Evaluate side-chains 59 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1429 time to fit residues: 1.8448 ------------------------------------------------------------------------------- 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: 0.8980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 6595 Z= 0.230 Angle : 0.581 7.421 8908 Z= 0.307 Chirality : 0.045 0.157 991 Planarity : 0.003 0.043 1140 Dihedral : 5.804 22.055 877 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.97 % Favored : 89.90 % Rotamer Outliers : 0.28 % 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: -1.95 (0.29), residues: 782 helix: -1.43 (0.47), residues: 107 sheet: -1.67 (0.46), residues: 103 loop : -1.25 (0.26), residues: 572 *********************** 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 58 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.031 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: 2 outliers final: 2 residues processed: 57 average time/residue: 0.4047 time to fit residues: 31.8978 Evaluate side-chains 57 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 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: 0.2038 time to fit residues: 2.0182 ------------------------------------------------------------------------------- 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: 0.6980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 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 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6595 Z= 0.199 Angle : 0.558 5.717 8908 Z= 0.295 Chirality : 0.045 0.148 991 Planarity : 0.003 0.043 1140 Dihedral : 5.624 22.099 877 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.70 % Favored : 91.18 % 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: -1.94 (0.29), residues: 782 helix: -1.33 (0.48), residues: 107 sheet: -1.58 (0.48), residues: 98 loop : -1.28 (0.26), residues: 577 *********************** 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 65 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 1.078 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 revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.4378 time to fit residues: 37.3642 Evaluate side-chains 59 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.991 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2187 time to fit residues: 1.9342 ------------------------------------------------------------------------------- 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: 0.6980 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.0040 chunk 65 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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** B 333 ASN B 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 6595 Z= 0.158 Angle : 0.542 5.398 8908 Z= 0.286 Chirality : 0.044 0.189 991 Planarity : 0.003 0.040 1140 Dihedral : 5.447 21.674 877 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.80 % Favored : 92.07 % Rotamer Outliers : 0.28 % 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: -1.91 (0.29), residues: 782 helix: -1.21 (0.49), residues: 107 sheet: -1.58 (0.48), residues: 98 loop : -1.28 (0.26), residues: 577 ********************** 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 64 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 1.085 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: 2 outliers final: 1 residues processed: 64 average time/residue: 0.4669 time to fit residues: 39.3135 Evaluate side-chains 62 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.070 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2692 time to fit residues: 1.7384 ------------------------------------------------------------------------------- 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: 1.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3872 r_free = 0.3872 target = 0.103436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.087212 restraints weight = 48323.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.090974 restraints weight = 22756.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.093548 restraints weight = 13568.492| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6595 Z= 0.175 Angle : 0.550 5.228 8908 Z= 0.289 Chirality : 0.044 0.145 991 Planarity : 0.003 0.041 1140 Dihedral : 5.422 21.466 877 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.44 % Favored : 91.43 % 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: -1.89 (0.29), residues: 782 helix: -1.06 (0.49), residues: 107 sheet: -1.61 (0.47), residues: 102 loop : -1.28 (0.26), residues: 573 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3509.19 seconds wall clock time: 62 minutes 32.15 seconds (3752.15 seconds total)