Starting phenix.real_space_refine on Thu Feb 15 16:23:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwi_21417/02_2024/6vwi_21417_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwi_21417/02_2024/6vwi_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_21417/02_2024/6vwi_21417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwi_21417/02_2024/6vwi_21417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwi_21417/02_2024/6vwi_21417_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwi_21417/02_2024/6vwi_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 9 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.87, 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: 10.42 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.24 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: 5.06 Time building geometry restraints manager: 10.72 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: 5496 17.65 - 35.30: 436 35.30 - 52.95: 124 52.95 - 70.60: 82 70.60 - 88.25: 12 Dihedral angle restraints: 6150 sinusoidal: 3404 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 6147 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: 2.690 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: 0.210 Extract box with map and model: 13.600 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 43.920 Find NCS groups from input model: 0.220 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.710 ------------------------------------------------------------------------------- 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 : 14.894 88.250 2524 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 % Allowed : 6.60 % Favored : 91.43 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.007 TRP A 176 HIS 0.009 0.003 HIS A 362 PHE 0.022 0.004 PHE A 45 TYR 0.040 0.007 TYR A 138 ARG 0.080 0.013 ARG A 104 *********************** 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 : 1.087 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: A 83 TYR cc_start: 0.8325 (t80) cc_final: 0.8116 (t80) REVERT: A 256 LEU cc_start: 0.8342 (tp) cc_final: 0.7776 (pt) REVERT: A 266 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.4319 (t80) REVERT: A 333 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7500 (t0) REVERT: B 396 GLN cc_start: 0.7956 (mt0) cc_final: 0.7691 (mt0) REVERT: B 572 LEU cc_start: 0.8623 (tp) cc_final: 0.8322 (tp) REVERT: I 44 GLU cc_start: 0.7835 (tt0) cc_final: 0.7278 (tt0) outliers start: 14 outliers final: 3 residues processed: 148 average time/residue: 0.4691 time to fit residues: 87.9374 Evaluate side-chains 80 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain I residue 8 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.0770 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 374 ASN B 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6595 Z= 0.216 Angle : 0.669 8.138 8908 Z= 0.363 Chirality : 0.047 0.167 991 Planarity : 0.004 0.033 1140 Dihedral : 8.793 55.570 970 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.53 % Allowed : 11.10 % Favored : 86.38 % 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: -1.80 (0.29), residues: 782 helix: -2.11 (0.46), residues: 108 sheet: -0.97 (0.45), residues: 115 loop : -1.09 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 402 HIS 0.004 0.001 HIS A 362 PHE 0.016 0.002 PHE A 326 TYR 0.009 0.001 TYR B 391 ARG 0.003 0.001 ARG B 474 *********************** 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 109 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 1.130 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 REVERT: A 312 ASP cc_start: 0.6645 (t0) cc_final: 0.6147 (t0) REVERT: A 333 ASN cc_start: 0.7532 (t0) cc_final: 0.7258 (t0) REVERT: A 439 LYS cc_start: 0.7975 (mttt) cc_final: 0.6884 (tptt) REVERT: B 406 HIS cc_start: 0.6673 (OUTLIER) cc_final: 0.6366 (m-70) REVERT: B 420 PHE cc_start: 0.7629 (m-80) cc_final: 0.7411 (m-80) REVERT: I 44 GLU cc_start: 0.7914 (tt0) cc_final: 0.7505 (tt0) outliers start: 18 outliers final: 15 residues processed: 104 average time/residue: 0.4049 time to fit residues: 56.0613 Evaluate side-chains 88 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 674 LYS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU 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: 0.5980 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 396 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3603 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= 0.215 Angle : 0.607 5.692 8908 Z= 0.329 Chirality : 0.046 0.172 991 Planarity : 0.003 0.031 1140 Dihedral : 7.869 55.260 965 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.53 % Allowed : 12.50 % Favored : 84.97 % 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: -1.69 (0.30), residues: 782 helix: -1.63 (0.49), residues: 108 sheet: -1.19 (0.42), residues: 125 loop : -1.01 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 402 HIS 0.003 0.001 HIS A 362 PHE 0.014 0.001 PHE A 45 TYR 0.012 0.001 TYR B 391 ARG 0.002 0.000 ARG B 565 *********************** 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 92 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.089 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: A 439 LYS cc_start: 0.8008 (mttt) cc_final: 0.7411 (mmtt) REVERT: B 333 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7443 (m-40) REVERT: B 406 HIS cc_start: 0.6718 (OUTLIER) cc_final: 0.6482 (m-70) REVERT: B 496 TYR cc_start: 0.8959 (m-80) cc_final: 0.8506 (m-10) REVERT: I 44 GLU cc_start: 0.7980 (tt0) cc_final: 0.7536 (tt0) outliers start: 18 outliers final: 8 residues processed: 88 average time/residue: 0.3468 time to fit residues: 42.1365 Evaluate side-chains 75 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4091 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= 0.285 Angle : 0.624 5.707 8908 Z= 0.336 Chirality : 0.046 0.159 991 Planarity : 0.004 0.040 1140 Dihedral : 7.829 57.023 965 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 3.65 % Allowed : 14.33 % Favored : 82.02 % 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: -1.98 (0.29), residues: 782 helix: -1.81 (0.46), residues: 107 sheet: -1.54 (0.42), residues: 120 loop : -1.20 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 402 HIS 0.002 0.001 HIS A 362 PHE 0.016 0.002 PHE A 45 TYR 0.016 0.001 TYR B 391 ARG 0.002 0.000 ARG A 108 *********************** 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 95 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 69 time to evaluate : 1.132 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 REVERT: A 394 ASP cc_start: 0.7295 (t0) cc_final: 0.6897 (t0) REVERT: A 439 LYS cc_start: 0.7993 (mttt) cc_final: 0.7206 (mmtt) REVERT: B 333 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7588 (m-40) REVERT: B 402 TRP cc_start: 0.6641 (OUTLIER) cc_final: 0.5892 (p-90) REVERT: I 44 GLU cc_start: 0.8039 (tt0) cc_final: 0.7631 (tt0) outliers start: 26 outliers final: 15 residues processed: 89 average time/residue: 0.4278 time to fit residues: 50.2291 Evaluate side-chains 81 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 60 CYS 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: 0.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6595 Z= 0.201 Angle : 0.577 5.436 8908 Z= 0.312 Chirality : 0.046 0.171 991 Planarity : 0.003 0.041 1140 Dihedral : 7.410 53.578 965 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.37 % Allowed : 14.04 % Favored : 82.58 % 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 (0.30), residues: 782 helix: -1.70 (0.47), residues: 107 sheet: -1.63 (0.42), residues: 120 loop : -1.12 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 402 HIS 0.005 0.001 HIS A 202 PHE 0.010 0.001 PHE A 45 TYR 0.011 0.001 TYR B 391 ARG 0.001 0.000 ARG I 49 *********************** 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 92 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 68 time to evaluate : 1.064 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7744 (mp) REVERT: B 387 ASN cc_start: 0.4123 (OUTLIER) cc_final: 0.2541 (t0) REVERT: B 402 TRP cc_start: 0.6702 (OUTLIER) cc_final: 0.5820 (p-90) REVERT: B 496 TYR cc_start: 0.8978 (m-80) cc_final: 0.8510 (m-10) outliers start: 24 outliers final: 16 residues processed: 87 average time/residue: 0.4477 time to fit residues: 50.5760 Evaluate side-chains 82 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 75 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7389 moved from start: 0.4646 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= 0.186 Angle : 0.545 5.089 8908 Z= 0.293 Chirality : 0.045 0.147 991 Planarity : 0.003 0.042 1140 Dihedral : 7.061 53.623 963 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.09 % Allowed : 14.75 % Favored : 82.16 % 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: -1.90 (0.30), residues: 782 helix: -1.63 (0.47), residues: 107 sheet: -1.65 (0.42), residues: 120 loop : -1.12 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 402 HIS 0.002 0.001 HIS A 362 PHE 0.010 0.001 PHE A 45 TYR 0.010 0.001 TYR B 391 ARG 0.002 0.000 ARG A 245 *********************** 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 89 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 1.062 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 revert: symmetry clash REVERT: B 311 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7818 (mp) REVERT: B 387 ASN cc_start: 0.4035 (OUTLIER) cc_final: 0.2697 (t0) REVERT: B 402 TRP cc_start: 0.6732 (OUTLIER) cc_final: 0.5910 (p-90) REVERT: B 496 TYR cc_start: 0.8974 (m-80) cc_final: 0.8465 (m-10) outliers start: 22 outliers final: 15 residues processed: 84 average time/residue: 0.4002 time to fit residues: 45.5914 Evaluate side-chains 83 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7373 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6595 Z= 0.160 Angle : 0.533 4.839 8908 Z= 0.285 Chirality : 0.044 0.155 991 Planarity : 0.003 0.043 1140 Dihedral : 6.721 54.071 963 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.80 % Favored : 92.07 % Rotamer: Outliers : 2.95 % Allowed : 15.45 % Favored : 81.60 % 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 (0.30), residues: 782 helix: -1.47 (0.48), residues: 107 sheet: -1.59 (0.42), residues: 120 loop : -1.08 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 402 HIS 0.002 0.000 HIS A 362 PHE 0.009 0.001 PHE B 420 TYR 0.009 0.001 TYR B 391 ARG 0.001 0.000 ARG A 245 *********************** 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 93 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 1.181 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 revert: symmetry clash revert: symmetry clash REVERT: A 402 TRP cc_start: 0.5709 (OUTLIER) cc_final: 0.5491 (p-90) REVERT: B 387 ASN cc_start: 0.4307 (OUTLIER) cc_final: 0.2997 (t0) REVERT: B 402 TRP cc_start: 0.6651 (OUTLIER) cc_final: 0.5923 (p-90) outliers start: 21 outliers final: 16 residues processed: 88 average time/residue: 0.4219 time to fit residues: 49.0921 Evaluate side-chains 88 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 69 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 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: 1.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6595 Z= 0.198 Angle : 0.543 4.928 8908 Z= 0.291 Chirality : 0.045 0.150 991 Planarity : 0.003 0.044 1140 Dihedral : 6.776 53.233 963 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.82 % Favored : 91.05 % Rotamer: Outliers : 3.09 % Allowed : 15.31 % Favored : 81.60 % 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: -1.83 (0.30), residues: 782 helix: -1.46 (0.48), residues: 107 sheet: -1.66 (0.42), residues: 120 loop : -1.09 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 402 HIS 0.002 0.001 HIS A 362 PHE 0.012 0.001 PHE A 45 TYR 0.011 0.001 TYR B 391 ARG 0.002 0.000 ARG A 108 *********************** 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 87 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 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 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: A 439 LYS cc_start: 0.7916 (mttt) cc_final: 0.7336 (mmmt) REVERT: B 311 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 387 ASN cc_start: 0.4559 (OUTLIER) cc_final: 0.3187 (t0) REVERT: B 402 TRP cc_start: 0.6801 (OUTLIER) cc_final: 0.5895 (p-90) REVERT: B 432 MET cc_start: 0.7877 (tmm) cc_final: 0.7677 (tmm) outliers start: 22 outliers final: 17 residues processed: 81 average time/residue: 0.4516 time to fit residues: 48.8138 Evaluate side-chains 83 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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: 0.7382 moved from start: 0.5154 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= 0.163 Angle : 0.528 4.772 8908 Z= 0.282 Chirality : 0.044 0.147 991 Planarity : 0.003 0.044 1140 Dihedral : 6.574 53.877 963 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.67 % Favored : 92.20 % Rotamer: Outliers : 3.23 % Allowed : 15.03 % Favored : 81.74 % 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: -1.78 (0.30), residues: 782 helix: -1.35 (0.48), residues: 107 sheet: -1.61 (0.43), residues: 120 loop : -1.07 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 402 HIS 0.003 0.000 HIS A 362 PHE 0.009 0.001 PHE A 45 TYR 0.011 0.001 TYR B 496 ARG 0.002 0.000 ARG B 376 *********************** 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 87 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 1.100 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 TRP cc_start: 0.5679 (OUTLIER) cc_final: 0.5460 (p-90) REVERT: A 439 LYS cc_start: 0.7885 (mttt) cc_final: 0.7315 (mmmt) REVERT: B 387 ASN cc_start: 0.4520 (OUTLIER) cc_final: 0.3240 (t0) REVERT: B 402 TRP cc_start: 0.6724 (OUTLIER) cc_final: 0.5936 (p-90) outliers start: 23 outliers final: 18 residues processed: 82 average time/residue: 0.4666 time to fit residues: 49.5426 Evaluate side-chains 86 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 0.0070 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6595 Z= 0.153 Angle : 0.516 4.499 8908 Z= 0.275 Chirality : 0.044 0.149 991 Planarity : 0.003 0.042 1140 Dihedral : 6.329 54.247 963 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.42 % Favored : 92.46 % Rotamer: Outliers : 2.25 % Allowed : 15.73 % Favored : 82.02 % 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: -1.68 (0.30), residues: 782 helix: -1.22 (0.49), residues: 107 sheet: -1.51 (0.45), residues: 116 loop : -1.03 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 402 HIS 0.002 0.000 HIS A 362 PHE 0.009 0.001 PHE I 19 TYR 0.011 0.001 TYR B 550 ARG 0.001 0.000 ARG A 245 ********************** 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 88 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.103 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 revert: symmetry clash revert: symmetry clash REVERT: A 402 TRP cc_start: 0.5662 (OUTLIER) cc_final: 0.5448 (p-90) REVERT: A 439 LYS cc_start: 0.7874 (mttt) cc_final: 0.7450 (mmmt) REVERT: B 387 ASN cc_start: 0.4388 (OUTLIER) cc_final: 0.3227 (t0) REVERT: B 402 TRP cc_start: 0.6656 (OUTLIER) cc_final: 0.5912 (p-90) REVERT: I 44 GLU cc_start: 0.7727 (tt0) cc_final: 0.7319 (tt0) outliers start: 16 outliers final: 13 residues processed: 86 average time/residue: 0.5218 time to fit residues: 59.6415 Evaluate side-chains 82 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.104479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.087934 restraints weight = 48492.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.091742 restraints weight = 22727.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.094298 restraints weight = 13568.597| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6595 Z= 0.204 Angle : 0.544 4.833 8908 Z= 0.289 Chirality : 0.044 0.146 991 Planarity : 0.003 0.044 1140 Dihedral : 6.546 53.392 963 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.44 % Favored : 91.43 % Rotamer: Outliers : 2.81 % Allowed : 15.45 % Favored : 81.74 % 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: -1.78 (0.30), residues: 782 helix: -1.27 (0.49), residues: 107 sheet: -1.57 (0.47), residues: 109 loop : -1.12 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 402 HIS 0.003 0.001 HIS A 362 PHE 0.012 0.001 PHE A 45 TYR 0.016 0.001 TYR B 550 ARG 0.001 0.000 ARG A 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3739.52 seconds wall clock time: 66 minutes 42.10 seconds (4002.10 seconds total)