Starting phenix.real_space_refine on Fri Feb 16 13:49:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0q_24791/02_2024/7s0q_24791_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0q_24791/02_2024/7s0q_24791.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/7s0q_24791/02_2024/7s0q_24791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0q_24791/02_2024/7s0q_24791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0q_24791/02_2024/7s0q_24791_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0q_24791/02_2024/7s0q_24791_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= -0.000 sd= 0.012 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 61 5.16 5 C 4970 2.51 5 N 1334 2.21 5 O 1526 1.98 5 H 7466 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 68": "OD1" <-> "OD2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 394": "OD1" <-> "OD2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B ASP 519": "OD1" <-> "OD2" Residue "B ASP 535": "OD1" <-> "OD2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15357 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 9039 Classifications: {'peptide': 575} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 549} Chain breaks: 1 Chain: "B" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5190 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 13, 'TRANS': 308} Chain breaks: 1 Chain: "D" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 913 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" 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 Time building chain proxies: 7.02, per 1000 atoms: 0.46 Number of scatterers: 15357 At special positions: 0 Unit cell: (85.86, 110.24, 108.12, 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 61 16.00 O 1526 8.00 N 1334 7.00 C 4970 6.00 H 7466 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, 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=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.04 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 458 " distance=2.04 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS B 524 " distance=2.04 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 52 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A1003 " - " ASN A 408 " " NAG A1004 " - " ASN A 504 " " NAG A1005 " - " ASN A 577 " " NAG B1001 " - " ASN B 337 " " NAG B1002 " - " ASN B 397 " " NAG B1003 " - " ASN B 514 " " NAG C 1 " - " ASN A 105 " " NAG E 1 " - " ASN A 21 " " NAG F 1 " - " ASN A 214 " Time building additional restraints: 12.86 Conformation dependent library (CDL) restraints added in 1.6 seconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 19 sheets defined 18.8% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.541A pdb=" N GLU A 20 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 4.589A pdb=" N ARG A 41 " --> pdb=" O GLU A 38 " (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 removed outlier: 3.604A pdb=" N ASN A 136 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.711A pdb=" N GLU A 147 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.583A pdb=" N ASN A 198 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 199' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 314 through 319 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.670A pdb=" N GLU A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 4.250A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 437 removed outlier: 4.136A pdb=" N ILE A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 330 removed outlier: 3.612A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 359 Processing helix chain 'B' and resid 435 through 446 removed outlier: 4.059A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 689 through 714 removed outlier: 4.298A pdb=" N LEU B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 708 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE B 714 " --> pdb=" O HIS B 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 19 removed outlier: 3.594A pdb=" N VAL D 11 " --> pdb=" O GLY D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 53 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.508A pdb=" N ILE A 76 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.483A pdb=" N LEU A 29 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE A 58 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 140 " --> pdb=" O ILE A 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 209 removed outlier: 5.641A pdb=" N LEU A 206 " --> pdb=" O CYS A 221 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N CYS A 221 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER A 208 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA9, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.898A pdb=" N LEU A 331 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG A 361 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE A 332 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 358 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU A 393 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 360 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR A 388 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TYR A 417 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 390 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.713A pdb=" N ILE A 378 " --> pdb=" O THR A 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 465 through 470 Processing sheet with id=AB3, first strand: chain 'A' and resid 520 through 525 removed outlier: 4.054A pdb=" N SER A 492 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 554 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 520 through 525 removed outlier: 4.054A pdb=" N SER A 492 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 554 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 311 through 321 removed outlier: 11.004A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 11.317A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS B 319 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS B 369 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B 340 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ARG B 371 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE B 342 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU B 368 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N LEU B 403 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 370 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 363 through 364 Processing sheet with id=AB7, first strand: chain 'B' and resid 471 through 472 removed outlier: 6.041A pdb=" N GLU B 471 " --> pdb=" O LYS B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AB9, first strand: chain 'B' and resid 530 through 534 Processing sheet with id=AC1, first strand: chain 'B' and resid 530 through 534 181 hydrogen bonds defined for protein. 453 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: 6.29 Time building geometry restraints manager: 13.41 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: 7463 1.03 - 1.23: 156 1.23 - 1.43: 3274 1.43 - 1.63: 4556 1.63 - 1.82: 77 Bond restraints: 15526 Sorted by residual: bond pdb=" C1 NAG B1003 " pdb=" O5 NAG B1003 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C1 NAG A1004 " pdb=" O5 NAG A1004 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C1 NAG A1005 " pdb=" O5 NAG A1005 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.48e+00 bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.40e+00 ... (remaining 15521 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.74: 235 106.74 - 113.54: 18080 113.54 - 120.35: 5035 120.35 - 127.15: 4462 127.15 - 133.95: 89 Bond angle restraints: 27901 Sorted by residual: angle pdb=" C ILE A 31 " pdb=" N LEU A 32 " pdb=" CA LEU A 32 " ideal model delta sigma weight residual 121.91 116.32 5.59 2.03e+00 2.43e-01 7.57e+00 angle pdb=" N CYS A 152 " pdb=" CA CYS A 152 " pdb=" C CYS A 152 " ideal model delta sigma weight residual 108.07 110.41 -2.34 8.90e-01 1.26e+00 6.94e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.43 6.52 3.00e+00 1.11e-01 4.73e+00 angle pdb=" C TRP A 244 " pdb=" N ARG A 245 " pdb=" CA ARG A 245 " ideal model delta sigma weight residual 122.33 118.68 3.65 1.68e+00 3.54e-01 4.71e+00 angle pdb=" CA VAL B 712 " pdb=" C VAL B 712 " pdb=" N VAL B 713 " ideal model delta sigma weight residual 116.60 119.74 -3.14 1.45e+00 4.76e-01 4.69e+00 ... (remaining 27896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 7093 22.14 - 44.28: 389 44.28 - 66.42: 77 66.42 - 88.56: 25 88.56 - 110.70: 23 Dihedral angle restraints: 7607 sinusoidal: 4295 harmonic: 3312 Sorted by residual: dihedral pdb=" CB CYS D 6 " pdb=" SG CYS D 6 " pdb=" SG CYS D 48 " pdb=" CB CYS D 48 " ideal model delta sinusoidal sigma weight residual 93.00 172.66 -79.66 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS A 205 " pdb=" SG CYS A 205 " pdb=" SG CYS A 218 " pdb=" CB CYS A 218 " ideal model delta sinusoidal sigma weight residual 93.00 165.84 -72.84 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " pdb=" SG CYS A 291 " pdb=" CB CYS A 291 " ideal model delta sinusoidal sigma weight residual 93.00 162.85 -69.85 1 1.00e+01 1.00e-02 6.29e+01 ... (remaining 7604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 1226 0.236 - 0.471: 5 0.471 - 0.707: 0 0.707 - 0.943: 0 0.943 - 1.179: 1 Chirality restraints: 1232 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.22 -1.18 2.00e-02 2.50e+03 3.47e+03 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.65e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.69e+01 ... (remaining 1229 not shown) Planarity restraints: 2308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 202 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 203 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 4 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.12e-01 pdb=" N PRO A 5 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 5 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 5 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 308 " 0.014 5.00e-02 4.00e+02 2.14e-02 7.35e-01 pdb=" N PRO B 309 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO B 309 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 309 " 0.012 5.00e-02 4.00e+02 ... (remaining 2305 not shown) Histogram of nonbonded interaction distances: 0.59 - 1.39: 1 1.39 - 2.19: 1175 2.19 - 3.00: 45446 3.00 - 3.80: 62621 3.80 - 4.60: 106415 Warning: very small nonbonded interaction distances. Nonbonded interactions: 215658 Sorted by model distance: nonbonded pdb="HD22 ASN A 387 " pdb=" C1 NAG A1002 " model vdw 0.590 2.750 nonbonded pdb=" ND2 ASN A 387 " pdb=" C1 NAG A1002 " model vdw 1.445 3.250 nonbonded pdb="HH11 ARG B 488 " pdb=" O HIS B 548 " model vdw 1.547 1.850 nonbonded pdb=" H THR B 560 " pdb=" OG1 THR B 590 " model vdw 1.553 1.850 nonbonded pdb=" H LYS A 115 " pdb=" O GLY A 141 " model vdw 1.559 1.850 ... (remaining 215653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' } 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: 6.970 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: 0.000 Extract box with map and model: 15.640 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 52.530 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 : 0.004 0.028 8060 Z= 0.238 Angle : 0.606 6.523 10912 Z= 0.319 Chirality : 0.057 1.179 1232 Planarity : 0.003 0.045 1387 Dihedral : 16.050 110.700 3252 Min Nonbonded Distance : 1.445 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.22), residues: 948 helix: -3.88 (0.27), residues: 129 sheet: -3.07 (0.35), residues: 154 loop : -3.50 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS A 480 PHE 0.011 0.001 PHE A 45 TYR 0.011 0.001 TYR A 85 ARG 0.003 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.358 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.6059 time to fit residues: 83.3686 Evaluate side-chains 76 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS A 254 ASN A 275 GLN A 287 GLN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 417 HIS ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8060 Z= 0.274 Angle : 0.639 7.379 10912 Z= 0.321 Chirality : 0.047 0.518 1232 Planarity : 0.004 0.052 1387 Dihedral : 13.127 96.284 1386 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 0.47 % Allowed : 7.85 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.23), residues: 948 helix: -2.42 (0.38), residues: 132 sheet: -2.84 (0.37), residues: 156 loop : -3.14 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 176 HIS 0.007 0.001 HIS A 362 PHE 0.015 0.001 PHE A 45 TYR 0.011 0.001 TYR A 85 ARG 0.010 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 1.191 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 GLU cc_start: 0.8162 (tt0) cc_final: 0.7947 (tp30) REVERT: D 46 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7075 (mm-30) outliers start: 4 outliers final: 1 residues processed: 77 average time/residue: 0.5159 time to fit residues: 52.4997 Evaluate side-chains 73 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8060 Z= 0.180 Angle : 0.562 5.448 10912 Z= 0.283 Chirality : 0.045 0.378 1232 Planarity : 0.003 0.053 1387 Dihedral : 10.097 84.750 1386 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.59 % Allowed : 9.25 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.24), residues: 948 helix: -1.88 (0.42), residues: 132 sheet: -2.82 (0.38), residues: 141 loop : -2.77 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS A 202 PHE 0.014 0.001 PHE A 45 TYR 0.008 0.001 TYR A 85 ARG 0.004 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 1.269 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7401 (pp) REVERT: A 381 GLU cc_start: 0.8133 (tt0) cc_final: 0.7919 (tp30) REVERT: B 587 TYR cc_start: 0.4232 (m-80) cc_final: 0.3886 (m-10) REVERT: D 46 GLU cc_start: 0.7689 (mt-10) cc_final: 0.6994 (mm-30) outliers start: 5 outliers final: 2 residues processed: 81 average time/residue: 0.5492 time to fit residues: 58.1301 Evaluate side-chains 77 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain B residue 542 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8060 Z= 0.189 Angle : 0.554 6.533 10912 Z= 0.281 Chirality : 0.044 0.422 1232 Planarity : 0.003 0.053 1387 Dihedral : 8.527 67.221 1386 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.59 % Allowed : 10.30 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.25), residues: 948 helix: -1.66 (0.42), residues: 132 sheet: -2.77 (0.39), residues: 136 loop : -2.57 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS B 440 PHE 0.014 0.001 PHE A 45 TYR 0.010 0.001 TYR A 85 ARG 0.002 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 1.353 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7401 (pp) REVERT: A 381 GLU cc_start: 0.8165 (tt0) cc_final: 0.7947 (tp30) REVERT: D 46 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7039 (mm-30) outliers start: 5 outliers final: 4 residues processed: 77 average time/residue: 0.5834 time to fit residues: 57.9440 Evaluate side-chains 78 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain B residue 542 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8060 Z= 0.155 Angle : 0.528 5.344 10912 Z= 0.269 Chirality : 0.044 0.353 1232 Planarity : 0.003 0.052 1387 Dihedral : 7.409 54.466 1386 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.47 % Allowed : 11.01 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.25), residues: 948 helix: -1.47 (0.43), residues: 133 sheet: -2.44 (0.39), residues: 149 loop : -2.45 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 176 HIS 0.003 0.001 HIS A 539 PHE 0.013 0.001 PHE A 45 TYR 0.008 0.001 TYR A 85 ARG 0.003 0.000 ARG D 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.227 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7355 (pp) REVERT: D 46 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7027 (tp30) outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.5874 time to fit residues: 56.7186 Evaluate side-chains 74 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 468 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8060 Z= 0.161 Angle : 0.520 5.456 10912 Z= 0.266 Chirality : 0.043 0.378 1232 Planarity : 0.003 0.049 1387 Dihedral : 6.209 45.264 1386 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 1.05 % Allowed : 11.12 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.25), residues: 948 helix: -1.28 (0.43), residues: 133 sheet: -2.29 (0.40), residues: 146 loop : -2.33 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS B 440 PHE 0.012 0.001 PHE A 45 TYR 0.010 0.001 TYR A 85 ARG 0.002 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 1.316 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7413 (pp) REVERT: D 46 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7048 (tp30) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.5811 time to fit residues: 60.2712 Evaluate side-chains 79 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain D residue 43 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 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 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 417 HIS ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8060 Z= 0.164 Angle : 0.518 5.104 10912 Z= 0.266 Chirality : 0.043 0.354 1232 Planarity : 0.003 0.045 1387 Dihedral : 5.439 35.252 1386 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 1.05 % Allowed : 11.36 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -2.99 (0.26), residues: 948 helix: -1.13 (0.44), residues: 133 sheet: -2.27 (0.38), residues: 156 loop : -2.22 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 176 HIS 0.004 0.001 HIS A 202 PHE 0.012 0.001 PHE A 45 TYR 0.008 0.001 TYR A 85 ARG 0.002 0.000 ARG D 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.190 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7034 (tp30) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.6307 time to fit residues: 63.2035 Evaluate side-chains 77 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain B residue 542 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8060 Z= 0.235 Angle : 0.565 6.291 10912 Z= 0.292 Chirality : 0.045 0.505 1232 Planarity : 0.003 0.047 1387 Dihedral : 5.688 40.474 1386 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.92 % Favored : 87.97 % Rotamer: Outliers : 0.82 % Allowed : 12.06 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.25), residues: 948 helix: -1.08 (0.44), residues: 131 sheet: -2.51 (0.40), residues: 130 loop : -2.29 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 176 HIS 0.005 0.001 HIS A 202 PHE 0.015 0.001 PHE A 45 TYR 0.011 0.001 TYR A 239 ARG 0.002 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 1.295 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: D 46 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7151 (tp30) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.6046 time to fit residues: 56.3373 Evaluate side-chains 69 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 468 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8060 Z= 0.211 Angle : 0.555 5.396 10912 Z= 0.288 Chirality : 0.044 0.414 1232 Planarity : 0.003 0.046 1387 Dihedral : 5.536 34.736 1386 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 0.70 % Allowed : 12.65 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -2.98 (0.26), residues: 948 helix: -0.86 (0.46), residues: 124 sheet: -2.50 (0.40), residues: 135 loop : -2.24 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 176 HIS 0.005 0.001 HIS A 539 PHE 0.015 0.001 PHE A 45 TYR 0.009 0.001 TYR A 85 ARG 0.004 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 1.366 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: D 46 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7341 (mm-30) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.6147 time to fit residues: 53.9681 Evaluate side-chains 66 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 468 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8060 Z= 0.167 Angle : 0.534 5.744 10912 Z= 0.276 Chirality : 0.043 0.366 1232 Planarity : 0.003 0.045 1387 Dihedral : 5.263 30.363 1386 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.70 % Allowed : 13.11 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -2.89 (0.26), residues: 948 helix: -0.76 (0.46), residues: 124 sheet: -2.41 (0.41), residues: 130 loop : -2.20 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 551 HIS 0.003 0.001 HIS A 539 PHE 0.014 0.001 PHE A 45 TYR 0.008 0.001 TYR A 85 ARG 0.006 0.000 ARG A 474 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 1.303 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: D 46 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7239 (mm-30) outliers start: 6 outliers final: 6 residues processed: 68 average time/residue: 0.6194 time to fit residues: 53.8303 Evaluate side-chains 67 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain B residue 586 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.0020 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** 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 = 0.3969 r_free = 0.3969 target = 0.077415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.068175 restraints weight = 122229.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.070525 restraints weight = 56502.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.071975 restraints weight = 32828.719| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8060 Z= 0.159 Angle : 0.529 5.614 10912 Z= 0.275 Chirality : 0.043 0.346 1232 Planarity : 0.003 0.044 1387 Dihedral : 5.068 28.940 1386 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 0.82 % Allowed : 12.76 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -2.80 (0.26), residues: 948 helix: -0.69 (0.46), residues: 124 sheet: -2.33 (0.40), residues: 145 loop : -2.12 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 176 HIS 0.003 0.001 HIS A 539 PHE 0.013 0.001 PHE A 45 TYR 0.008 0.001 TYR A 85 ARG 0.005 0.000 ARG A 474 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.32 seconds wall clock time: 68 minutes 32.27 seconds (4112.27 seconds total)