Starting phenix.real_space_refine on Fri Feb 16 16:18:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg1_22309/02_2024/7jg1_22309_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg1_22309/02_2024/7jg1_22309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg1_22309/02_2024/7jg1_22309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg1_22309/02_2024/7jg1_22309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg1_22309/02_2024/7jg1_22309_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg1_22309/02_2024/7jg1_22309_trim.pdb" } resolution = 3.3 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 5014 2.51 5 N 1341 2.21 5 O 1590 1.98 5 H 7808 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 283": "OD1" <-> "OD2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 34": "OE1" <-> "OE2" Residue "J GLU 75": "OE1" <-> "OE2" Residue "J TYR 104": "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: 15811 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3471 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 213} Chain: "B" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3374 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 17, 'TRANS': 206} Chain: "C" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3457 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 213} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3404 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 17, 'TRANS': 210} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2049 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 10, 'TRANS': 120} Chain breaks: 1 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: "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 Chain: "D" 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: 7.34, per 1000 atoms: 0.46 Number of scatterers: 15811 At special positions: 0 Unit cell: (154.66, 85.272, 131.252, 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 58 16.00 O 1590 8.00 N 1341 7.00 C 5014 6.00 H 7808 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 318 " distance=2.04 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 427 " distance=2.04 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 318 " distance=2.04 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 427 " distance=2.04 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS D 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 427 " distance=2.04 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS J 14 " distance=2.04 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS D 296 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 318 " distance=2.03 Simple disulfide: pdb=" SG CYS D 364 " - pdb=" SG CYS D 427 " distance=2.04 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 101 " distance=2.03 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.05 Simple disulfide: pdb=" SG CYS J 109 " - pdb=" SG CYS J 134 " 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 E 1 " - " NAG E 2 " NAG-ASN " NAG B 501 " - " ASN B 452 " " NAG D 501 " - " ASN D 452 " " NAG E 1 " - " ASN J 48 " Time building additional restraints: 12.59 Conformation dependent library (CDL) restraints added in 1.9 seconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 25 sheets defined 11.7% alpha, 46.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.677A pdb=" N LEU B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'D' and resid 248 through 253 Processing helix chain 'D' and resid 306 through 313 Processing helix chain 'D' and resid 350 through 356 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 415 through 422 Processing helix chain 'J' and resid 64 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 244 Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 244 Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 276 Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 347 removed outlier: 3.524A pdb=" N THR A 363 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR A 406 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 347 removed outlier: 3.524A pdb=" N THR A 363 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR A 406 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.635A pdb=" N SER A 426 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE A 438 " --> pdb=" O ALA J 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 453 through 460 removed outlier: 7.091A pdb=" N VAL A 453 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N SER B 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 455 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE B 458 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 457 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER B 460 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET A 459 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N PHE J 60 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER A 456 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N TYR J 62 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 458 " --> pdb=" O TYR J 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.756A pdb=" N THR B 260 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR B 297 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.756A pdb=" N THR B 260 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR B 297 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 276 Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 347 removed outlier: 3.711A pdb=" N THR B 363 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR B 406 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 407 " --> pdb=" O PRO B 395 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B 409 " --> pdb=" O PHE B 393 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 383 through 384 Processing sheet with id=AB4, first strand: chain 'C' and resid 240 through 244 removed outlier: 5.645A pdb=" N THR C 260 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU C 303 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR C 262 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N SER C 301 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN C 264 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 299 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 240 through 244 removed outlier: 5.645A pdb=" N THR C 260 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU C 303 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR C 262 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N SER C 301 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN C 264 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 299 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 273 through 276 Processing sheet with id=AB7, first strand: chain 'C' and resid 343 through 347 Processing sheet with id=AB8, first strand: chain 'C' and resid 343 through 347 Processing sheet with id=AB9, first strand: chain 'C' and resid 383 through 384 removed outlier: 3.629A pdb=" N LEU C 375 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE C 438 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU J 78 " --> pdb=" O GLN J 81 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 454 through 458 removed outlier: 3.760A pdb=" N THR J 18 " --> pdb=" O ASN J 36 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG J 16 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA J 8 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER J 19 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE J 6 " --> pdb=" O SER J 19 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 465 through 466 Processing sheet with id=AC3, first strand: chain 'D' and resid 240 through 244 removed outlier: 3.538A pdb=" N SER D 240 " --> pdb=" O ASN D 264 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR D 260 " --> pdb=" O LEU D 303 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU D 303 " --> pdb=" O THR D 260 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N THR D 262 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER D 301 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASN D 264 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL D 299 " --> pdb=" O ASN D 264 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 273 through 276 removed outlier: 4.217A pdb=" N VAL D 273 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR D 321 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR D 319 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 343 through 347 removed outlier: 3.521A pdb=" N GLN D 343 " --> pdb=" O ARG D 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 343 through 347 removed outlier: 3.521A pdb=" N GLN D 343 " --> pdb=" O ARG D 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 383 through 384 362 hydrogen bonds defined for protein. 939 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: 6.26 Time building geometry restraints manager: 13.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7804 1.02 - 1.22: 6 1.22 - 1.42: 3251 1.42 - 1.63: 4845 1.63 - 1.83: 75 Bond restraints: 15981 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" C2 NAG E 1 " ideal model delta sigma weight residual 1.532 1.652 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN A 268 " pdb="HD22 ASN A 268 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN A 268 " pdb="HD21 ASN A 268 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN J 48 " pdb="HD21 ASN J 48 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" N ALA A 272 " pdb=" CA ALA A 272 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.30e-02 5.92e+03 7.63e+00 ... (remaining 15976 not shown) Histogram of bond angle deviations from ideal: 76.54 - 88.11: 2 88.11 - 99.68: 5 99.68 - 111.26: 18292 111.26 - 122.83: 8473 122.83 - 134.41: 2226 Bond angle restraints: 28998 Sorted by residual: angle pdb=" CB MET B 428 " pdb=" CG MET B 428 " pdb=" HG3 MET B 428 " ideal model delta sigma weight residual 109.00 76.54 32.46 3.00e+00 1.11e-01 1.17e+02 angle pdb=" SD MET B 428 " pdb=" CG MET B 428 " pdb=" HG3 MET B 428 " ideal model delta sigma weight residual 108.00 76.57 31.43 3.00e+00 1.11e-01 1.10e+02 angle pdb=" C2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 110.06 88.39 21.67 3.00e+00 1.11e-01 5.22e+01 angle pdb=" C MET B 428 " pdb=" CA MET B 428 " pdb=" HA MET B 428 " ideal model delta sigma weight residual 110.00 91.03 18.97 3.00e+00 1.11e-01 4.00e+01 angle pdb=" CB GLN B 440 " pdb=" CG GLN B 440 " pdb=" HG2 GLN B 440 " ideal model delta sigma weight residual 109.00 92.79 16.21 3.00e+00 1.11e-01 2.92e+01 ... (remaining 28993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 7154 17.70 - 35.40: 385 35.40 - 53.11: 125 53.11 - 70.81: 43 70.81 - 88.51: 13 Dihedral angle restraints: 7720 sinusoidal: 4335 harmonic: 3385 Sorted by residual: dihedral pdb=" CB CYS C 237 " pdb=" SG CYS C 237 " pdb=" SG CYS C 296 " pdb=" CB CYS C 296 " ideal model delta sinusoidal sigma weight residual 93.00 170.77 -77.77 1 1.00e+01 1.00e-02 7.57e+01 dihedral pdb=" CB CYS C 466 " pdb=" SG CYS C 466 " pdb=" SG CYS J 14 " pdb=" CB CYS J 14 " ideal model delta sinusoidal sigma weight residual 93.00 167.27 -74.27 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS A 294 " pdb=" SG CYS A 294 " pdb=" SG CYS B 294 " pdb=" CB CYS B 294 " ideal model delta sinusoidal sigma weight residual -86.00 -36.18 -49.82 1 1.00e+01 1.00e-02 3.41e+01 ... (remaining 7717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 1316 0.203 - 0.405: 2 0.405 - 0.608: 0 0.608 - 0.811: 0 0.811 - 1.013: 2 Chirality restraints: 1320 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN J 48 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.41 1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 452 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.89e+01 ... (remaining 1317 not shown) Planarity restraints: 2405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 268 " -0.114 2.00e-02 2.50e+03 1.12e-01 1.88e+02 pdb=" CG ASN A 268 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 268 " 0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN A 268 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 268 " -0.160 2.00e-02 2.50e+03 pdb="HD22 ASN A 268 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 435 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" N MET B 436 " -0.069 2.00e-02 2.50e+03 pdb=" CA MET B 436 " 0.017 2.00e-02 2.50e+03 pdb=" H MET B 436 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 438 " -0.019 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" N THR B 439 " 0.060 2.00e-02 2.50e+03 pdb=" CA THR B 439 " -0.015 2.00e-02 2.50e+03 pdb=" H THR B 439 " -0.027 2.00e-02 2.50e+03 ... (remaining 2402 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.85: 46 1.85 - 2.54: 13915 2.54 - 3.23: 47787 3.23 - 3.91: 59867 3.91 - 4.60: 92663 Nonbonded interactions: 214278 Sorted by model distance: nonbonded pdb=" CG MET B 428 " pdb=" NE2 GLN B 440 " model vdw 1.169 3.250 nonbonded pdb=" HB2 GLU J 47 " pdb=" HG SER J 54 " model vdw 1.406 2.270 nonbonded pdb=" O PRO D 278 " pdb=" HG SER D 279 " model vdw 1.532 1.850 nonbonded pdb=" OE2 GLU C 353 " pdb="HH12 ARG C 413 " model vdw 1.561 1.850 nonbonded pdb=" OG SER J 50 " pdb=" C1 NAG E 1 " model vdw 1.584 3.100 ... (remaining 214273 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 'A' and (resid 237 through 371 or (resid 372 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 373 through 405 or (r \ esid 406 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 407 through 427 or (resid 428 and (name N or name CA or name C o \ r name O or name CB or name CG or name SD or name CE or name H or name HA or nam \ e HB2 or name HB3 or name HG3 or name HE1 or name HE2 or name HE3)) or resid 429 \ through 433 or (resid 434 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name H or name HA or name HB2 or name HB3 \ or name HG or name HD11 or name HD13 or name HD21 or name HD22 or name HD23)) o \ r resid 435 through 439 or (resid 440 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name OE1 or name NE2 or name H or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 441 through 451 or (re \ sid 452 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or \ resid 453 through 460)) selection = (chain 'B' and (resid 237 through 371 or (resid 372 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 373 through 405 or (r \ esid 406 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 407 through 460)) selection = (chain 'C' and (resid 237 through 371 or (resid 372 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 373 through 427 or (r \ esid 428 and (name N or name CA or name C or name O or name CB or name CG or nam \ e SD or name CE or name H or name HA or name HB2 or name HB3 or name HG3 or name \ HE1 or name HE2 or name HE3)) or resid 429 through 433 or (resid 434 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 o \ r name H or name HA or name HB2 or name HB3 or name HG or name HD11 or name HD13 \ or name HD21 or name HD22 or name HD23)) or resid 435 through 439 or (resid 440 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or \ name HG3)) or resid 441 through 451 or (resid 452 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 453 through 460)) selection = (chain 'D' and (resid 237 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 407 through 427 or (r \ esid 428 and (name N or name CA or name C or name O or name CB or name CG or nam \ e SD or name CE or name H or name HA or name HB2 or name HB3 or name HG3 or name \ HE1 or name HE2 or name HE3)) or resid 429 through 433 or (resid 434 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 o \ r name H or name HA or name HB2 or name HB3 or name HG or name HD11 or name HD13 \ or name HD21 or name HD22 or name HD23)) or resid 435 through 439 or (resid 440 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or \ name HG3)) or resid 441 through 460)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.270 Extract box with map and model: 10.770 Check model and map are aligned: 0.230 Set scattering table: 0.210 Process input model: 54.070 Find NCS groups from input model: 0.730 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 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 0.120 8173 Z= 0.231 Angle : 0.764 21.674 11155 Z= 0.405 Chirality : 0.059 1.013 1320 Planarity : 0.005 0.054 1441 Dihedral : 12.870 88.510 3074 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.33 % Allowed : 5.33 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.24), residues: 1033 helix: -3.51 (0.29), residues: 100 sheet: 0.91 (0.25), residues: 391 loop : -1.38 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 276 HIS 0.005 0.001 HIS D 431 PHE 0.014 0.002 PHE B 369 TYR 0.019 0.001 TYR A 390 ARG 0.002 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 265 time to evaluate : 1.216 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 411 VAL cc_start: 0.7883 (t) cc_final: 0.7650 (t) REVERT: B 292 ASN cc_start: 0.6560 (m-40) cc_final: 0.6172 (m-40) REVERT: C 244 GLN cc_start: 0.6727 (tp40) cc_final: 0.6219 (mp10) REVERT: C 451 THR cc_start: 0.7009 (m) cc_final: 0.6628 (m) REVERT: D 274 PHE cc_start: 0.4728 (p90) cc_final: 0.4417 (p90) REVERT: D 296 CYS cc_start: 0.5507 (m) cc_final: 0.4713 (m) REVERT: D 398 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7153 (mt-10) REVERT: J 21 ILE cc_start: 0.7732 (mm) cc_final: 0.6662 (mm) REVERT: J 57 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7299 (ttt-90) outliers start: 3 outliers final: 1 residues processed: 267 average time/residue: 0.4903 time to fit residues: 171.3785 Evaluate side-chains 154 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain J residue 57 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.0370 chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 ASN D 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8173 Z= 0.231 Angle : 0.671 5.800 11155 Z= 0.355 Chirality : 0.047 0.419 1320 Planarity : 0.006 0.045 1441 Dihedral : 6.837 51.833 1191 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 1.96 % Allowed : 11.75 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1033 helix: -2.31 (0.40), residues: 102 sheet: 0.95 (0.25), residues: 414 loop : -0.99 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 276 HIS 0.004 0.001 HIS J 119 PHE 0.017 0.002 PHE B 316 TYR 0.016 0.001 TYR A 390 ARG 0.002 0.000 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.258 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 287 LYS cc_start: 0.6247 (mttt) cc_final: 0.5793 (mmtt) REVERT: A 411 VAL cc_start: 0.8040 (t) cc_final: 0.7830 (t) REVERT: B 384 GLU cc_start: 0.6536 (pp20) cc_final: 0.6154 (tm-30) REVERT: C 244 GLN cc_start: 0.6766 (tp40) cc_final: 0.6329 (mp10) REVERT: C 317 LYS cc_start: 0.6297 (mptt) cc_final: 0.5722 (tptt) REVERT: D 296 CYS cc_start: 0.5621 (m) cc_final: 0.4631 (m) REVERT: D 301 SER cc_start: 0.6655 (m) cc_final: 0.6260 (t) REVERT: D 353 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7042 (mm-30) REVERT: J 18 THR cc_start: 0.7161 (p) cc_final: 0.6836 (p) outliers start: 18 outliers final: 16 residues processed: 170 average time/residue: 0.3822 time to fit residues: 91.7289 Evaluate side-chains 150 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 278 PRO Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 59 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 GLN C 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8173 Z= 0.287 Angle : 0.647 5.064 11155 Z= 0.338 Chirality : 0.046 0.353 1320 Planarity : 0.005 0.055 1441 Dihedral : 6.220 47.985 1187 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.52 % Favored : 94.39 % Rotamer: Outliers : 3.26 % Allowed : 11.97 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.25), residues: 1033 helix: -1.48 (0.48), residues: 103 sheet: 0.93 (0.25), residues: 401 loop : -0.84 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 276 HIS 0.005 0.001 HIS J 63 PHE 0.014 0.002 PHE B 369 TYR 0.010 0.002 TYR A 390 ARG 0.004 0.001 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 1.374 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: B 384 GLU cc_start: 0.6752 (pp20) cc_final: 0.6357 (tm-30) REVERT: B 428 MET cc_start: 0.6420 (ttp) cc_final: 0.6202 (mtm) REVERT: C 244 GLN cc_start: 0.6699 (tp40) cc_final: 0.6228 (mp10) REVERT: C 317 LYS cc_start: 0.6525 (mptt) cc_final: 0.6075 (tptt) REVERT: D 296 CYS cc_start: 0.5650 (m) cc_final: 0.5380 (m) REVERT: D 301 SER cc_start: 0.6707 (m) cc_final: 0.6331 (t) REVERT: D 353 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7117 (mm-30) REVERT: J 13 MET cc_start: 0.7617 (mtm) cc_final: 0.7256 (ptp) REVERT: J 78 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6299 (mp) outliers start: 30 outliers final: 26 residues processed: 166 average time/residue: 0.3773 time to fit residues: 87.2130 Evaluate side-chains 150 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN J 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8173 Z= 0.345 Angle : 0.684 6.691 11155 Z= 0.353 Chirality : 0.047 0.275 1320 Planarity : 0.006 0.054 1441 Dihedral : 6.251 54.760 1187 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.84 % Favored : 94.77 % Rotamer: Outliers : 3.81 % Allowed : 13.93 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1033 helix: -1.38 (0.49), residues: 103 sheet: 0.91 (0.25), residues: 406 loop : -0.95 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 276 HIS 0.006 0.001 HIS J 63 PHE 0.013 0.002 PHE C 340 TYR 0.016 0.002 TYR J 110 ARG 0.009 0.001 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 1.211 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: B 401 GLU cc_start: 0.5854 (tp30) cc_final: 0.5590 (tp30) REVERT: C 244 GLN cc_start: 0.6854 (tp40) cc_final: 0.6411 (mp10) REVERT: C 317 LYS cc_start: 0.6778 (mptt) cc_final: 0.6116 (tppt) REVERT: C 405 THR cc_start: 0.6826 (p) cc_final: 0.6604 (p) REVERT: D 296 CYS cc_start: 0.5924 (m) cc_final: 0.5448 (m) REVERT: D 301 SER cc_start: 0.6874 (m) cc_final: 0.6532 (t) REVERT: D 353 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7217 (mm-30) REVERT: J 13 MET cc_start: 0.7679 (mtm) cc_final: 0.7419 (ptp) outliers start: 35 outliers final: 22 residues processed: 154 average time/residue: 0.3875 time to fit residues: 82.6062 Evaluate side-chains 134 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 45 ASN Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 87 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN D 440 GLN J 36 ASN J 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8173 Z= 0.214 Angle : 0.595 5.663 11155 Z= 0.304 Chirality : 0.045 0.281 1320 Planarity : 0.006 0.057 1441 Dihedral : 5.607 43.656 1185 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.74 % Favored : 94.97 % Rotamer: Outliers : 2.83 % Allowed : 15.13 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1033 helix: -1.16 (0.50), residues: 104 sheet: 1.10 (0.26), residues: 400 loop : -0.73 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 276 HIS 0.004 0.001 HIS D 431 PHE 0.012 0.001 PHE C 340 TYR 0.015 0.001 TYR B 425 ARG 0.008 0.000 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.155 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: B 401 GLU cc_start: 0.5746 (tp30) cc_final: 0.5500 (tp30) REVERT: C 244 GLN cc_start: 0.6859 (tp40) cc_final: 0.6320 (mp10) REVERT: C 317 LYS cc_start: 0.6738 (mptt) cc_final: 0.6124 (tppt) REVERT: C 405 THR cc_start: 0.6831 (p) cc_final: 0.6612 (p) REVERT: D 296 CYS cc_start: 0.5832 (m) cc_final: 0.5542 (m) REVERT: D 301 SER cc_start: 0.6763 (m) cc_final: 0.6504 (t) REVERT: J 13 MET cc_start: 0.7830 (mtm) cc_final: 0.7611 (ptp) outliers start: 26 outliers final: 21 residues processed: 136 average time/residue: 0.4028 time to fit residues: 76.9539 Evaluate side-chains 130 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 119 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN J 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8173 Z= 0.260 Angle : 0.594 5.228 11155 Z= 0.305 Chirality : 0.044 0.234 1320 Planarity : 0.005 0.053 1441 Dihedral : 5.461 42.011 1185 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.03 % Favored : 94.68 % Rotamer: Outliers : 3.37 % Allowed : 14.25 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1033 helix: -1.16 (0.50), residues: 104 sheet: 1.01 (0.26), residues: 402 loop : -0.73 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 276 HIS 0.005 0.001 HIS D 431 PHE 0.012 0.001 PHE B 369 TYR 0.014 0.001 TYR C 297 ARG 0.008 0.001 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.218 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: A 405 THR cc_start: 0.7774 (p) cc_final: 0.7463 (p) REVERT: B 291 GLN cc_start: 0.6425 (pp30) cc_final: 0.6124 (pp30) REVERT: B 401 GLU cc_start: 0.5799 (tp30) cc_final: 0.5576 (tp30) REVERT: C 253 LEU cc_start: 0.8114 (tt) cc_final: 0.7780 (tp) REVERT: C 317 LYS cc_start: 0.6815 (mptt) cc_final: 0.6224 (tppt) REVERT: C 405 THR cc_start: 0.7138 (p) cc_final: 0.6905 (p) REVERT: D 296 CYS cc_start: 0.5744 (m) cc_final: 0.5453 (m) REVERT: J 13 MET cc_start: 0.7515 (mtm) cc_final: 0.7300 (ptp) outliers start: 31 outliers final: 23 residues processed: 142 average time/residue: 0.4203 time to fit residues: 81.5559 Evaluate side-chains 132 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 45 ASN Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.0000 chunk 56 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8173 Z= 0.175 Angle : 0.556 4.542 11155 Z= 0.284 Chirality : 0.044 0.234 1320 Planarity : 0.005 0.051 1441 Dihedral : 5.251 42.965 1185 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.74 % Favored : 94.97 % Rotamer: Outliers : 2.72 % Allowed : 15.56 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1033 helix: -0.59 (0.55), residues: 98 sheet: 1.12 (0.26), residues: 402 loop : -0.56 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 276 HIS 0.008 0.001 HIS D 431 PHE 0.010 0.001 PHE C 340 TYR 0.010 0.001 TYR C 297 ARG 0.007 0.000 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 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: A 459 MET cc_start: 0.7177 (tpt) cc_final: 0.6966 (tpt) REVERT: B 291 GLN cc_start: 0.6475 (pp30) cc_final: 0.6177 (pp30) REVERT: B 401 GLU cc_start: 0.5728 (tp30) cc_final: 0.5508 (tp30) REVERT: C 253 LEU cc_start: 0.8033 (tt) cc_final: 0.7733 (tp) REVERT: C 317 LYS cc_start: 0.6797 (mptt) cc_final: 0.6235 (tppt) REVERT: C 405 THR cc_start: 0.7183 (p) cc_final: 0.6951 (p) REVERT: D 296 CYS cc_start: 0.5691 (m) cc_final: 0.5425 (m) REVERT: J 13 MET cc_start: 0.7487 (mtm) cc_final: 0.7242 (ptp) outliers start: 25 outliers final: 23 residues processed: 131 average time/residue: 0.3736 time to fit residues: 69.6459 Evaluate side-chains 129 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 390 TYR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 125 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 380 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8173 Z= 0.329 Angle : 0.620 4.716 11155 Z= 0.319 Chirality : 0.045 0.215 1320 Planarity : 0.005 0.056 1441 Dihedral : 5.503 43.197 1185 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.10 % Favored : 93.51 % Rotamer: Outliers : 3.70 % Allowed : 14.80 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1033 helix: -1.13 (0.49), residues: 104 sheet: 0.87 (0.25), residues: 402 loop : -0.83 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 419 HIS 0.014 0.002 HIS D 431 PHE 0.015 0.002 PHE C 369 TYR 0.009 0.002 TYR C 425 ARG 0.004 0.000 ARG J 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 1.323 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: A 405 THR cc_start: 0.7735 (p) cc_final: 0.7441 (p) REVERT: B 291 GLN cc_start: 0.6489 (pp30) cc_final: 0.6229 (pp30) REVERT: B 401 GLU cc_start: 0.5969 (tp30) cc_final: 0.5741 (tp30) REVERT: C 317 LYS cc_start: 0.6897 (mptt) cc_final: 0.6469 (tppt) REVERT: C 373 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: C 405 THR cc_start: 0.7436 (p) cc_final: 0.7209 (p) REVERT: D 296 CYS cc_start: 0.5555 (m) cc_final: 0.5291 (m) outliers start: 34 outliers final: 31 residues processed: 141 average time/residue: 0.4108 time to fit residues: 80.1768 Evaluate side-chains 148 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 390 TYR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 463 ASP Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 45 ASN Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 125 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.7331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8173 Z= 0.193 Angle : 0.563 4.599 11155 Z= 0.288 Chirality : 0.044 0.218 1320 Planarity : 0.005 0.055 1441 Dihedral : 5.298 44.517 1185 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.94 % Favored : 94.68 % Rotamer: Outliers : 3.26 % Allowed : 15.89 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1033 helix: -0.66 (0.54), residues: 98 sheet: 1.00 (0.25), residues: 402 loop : -0.71 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 276 HIS 0.008 0.001 HIS D 431 PHE 0.016 0.001 PHE B 438 TYR 0.012 0.001 TYR A 297 ARG 0.002 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 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: A 405 THR cc_start: 0.7659 (p) cc_final: 0.7421 (p) REVERT: B 291 GLN cc_start: 0.6447 (pp30) cc_final: 0.6198 (pp30) REVERT: B 401 GLU cc_start: 0.5883 (tp30) cc_final: 0.5661 (tp30) REVERT: C 317 LYS cc_start: 0.6887 (mptt) cc_final: 0.6257 (tppt) REVERT: C 405 THR cc_start: 0.7427 (p) cc_final: 0.7202 (p) REVERT: D 296 CYS cc_start: 0.5484 (m) cc_final: 0.5234 (m) outliers start: 30 outliers final: 25 residues processed: 135 average time/residue: 0.4139 time to fit residues: 77.5871 Evaluate side-chains 136 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 390 TYR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 463 ASP Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.7513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8173 Z= 0.222 Angle : 0.567 5.313 11155 Z= 0.288 Chirality : 0.044 0.206 1320 Planarity : 0.005 0.055 1441 Dihedral : 5.215 42.451 1185 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.61 % Favored : 94.00 % Rotamer: Outliers : 2.94 % Allowed : 16.00 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1033 helix: -0.52 (0.55), residues: 98 sheet: 1.01 (0.25), residues: 403 loop : -0.67 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.010 0.001 HIS D 431 PHE 0.010 0.001 PHE C 369 TYR 0.008 0.001 TYR C 425 ARG 0.002 0.000 ARG C 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 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: A 405 THR cc_start: 0.7651 (p) cc_final: 0.7416 (p) REVERT: B 291 GLN cc_start: 0.6449 (pp30) cc_final: 0.6214 (pp30) REVERT: B 401 GLU cc_start: 0.5867 (tp30) cc_final: 0.5643 (tp30) REVERT: C 317 LYS cc_start: 0.6903 (mptt) cc_final: 0.6460 (tppt) REVERT: D 296 CYS cc_start: 0.5402 (m) cc_final: 0.5164 (m) outliers start: 27 outliers final: 24 residues processed: 128 average time/residue: 0.3863 time to fit residues: 68.7225 Evaluate side-chains 133 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 390 TYR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 463 ASP Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 45 ASN Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 71 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.187538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.146218 restraints weight = 26459.328| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.05 r_work: 0.3734 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.7592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8173 Z= 0.176 Angle : 0.544 4.862 11155 Z= 0.275 Chirality : 0.043 0.203 1320 Planarity : 0.005 0.055 1441 Dihedral : 5.045 41.063 1185 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.03 % Favored : 94.58 % Rotamer: Outliers : 2.72 % Allowed : 16.32 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1033 helix: -0.38 (0.55), residues: 98 sheet: 1.14 (0.25), residues: 403 loop : -0.56 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 276 HIS 0.007 0.001 HIS D 431 PHE 0.009 0.001 PHE C 340 TYR 0.009 0.001 TYR A 297 ARG 0.003 0.000 ARG C 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4567.97 seconds wall clock time: 81 minutes 2.88 seconds (4862.88 seconds total)